Package 'universalmotif' reference manual

Title:	Import, Modify, and Export Motifs with R
Description:	Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Authors:	Benjamin Jean-Marie Tremblay [aut, cre] , Spencer Nystrom [ctb]
Maintainer:	Benjamin Jean-Marie Tremblay <[email protected]>
License:	GPL-3
Version:	1.25.1
Built:	2024-11-12 03:25:18 UTC
Source:	https://github.com/bioc/universalmotif

Add multi-letter information to a motif.

Description

If the original sequences are available for a particular motif, then they can be used to generate higher-order PPM matrices. See the "Motif import, export, and manipulation" vignette for more information.

Usage

add_multifreq(motif, sequences, add.k = 2:3, RC = FALSE,
  threshold = 0.001, threshold.type = "pvalue", motifs.perseq = 1,
  add.bkg = FALSE)
add_multifreq(motif, sequences, add.k = 2:3, RC = FALSE,
  threshold = 0.001, threshold.type = "pvalue", motifs.perseq = 1,
  add.bkg = FALSE)

Arguments

`motif`	See `convert_motifs()` for acceptable formats. If the motif is not a universalmotif motif, then it will be converted.
`sequences`	`XStringSet` The alphabet must match that of the motif. If these sequences are all the same length as the motif, then they are all used to generate the multi-freq matrices. Otherwise `scan_sequences()` is first run to find the best sequence stretches within these.
`add.k`	`numeric(1)` The k-let lengths to add.
`RC`	`logical(1)` If `TRUE`, check reverse complement of the input sequences. Only available for DNA/RNA.
`threshold`	`numeric(1)` See details.
`threshold.type`	`character(1)` One of `c('pvalue', 'qvalue', 'logodds', 'logodds.abs')`. See details.
`motifs.perseq`	`numeric(1)` If `scan_sequences()` is run, then this indicates how many hits from each sequence is to be used.
`add.bkg`	`logical(1)` Indicate whether to add corresponding higher order background information to the motif. Can sometimes be detrimental when the input consists of few short sequences, which can increase the likelihood of adding zero or near-zero probabilities.

Details

See scan_sequences() for more info on scanning parameters.

At each position in the motif, then the probability of each k-let covering from the initial position to ncol - 1 is calculated. Only positions within the motif are considered: this means that the final k-let probability matrix will have ncol - 1 fewer columns. Calculating k-let probabilities for the missing columns would be trivial however, as you would only need the background frequencies. Since these would not be useful for scan_sequences() though, they are not calculated.

Currently add_multifreq() does not try to stay faithful to the default motif matrix when generating multifreq matrices. This means that if the sequences used for training are completely different from the actual motif, the multifreq matrices will be as well. However this is only really a problem if you supply add_multifreq() with a set of sequences of the same length as the motif. In this case add_multifreq() is forced to create the multifreq matrices from these sequences. Otherwise add_multifreq() will scan the input sequences for the motif and use the best matches to construct the multifreq matrices.

This 'multifreq' representation is only really useful within the universalmotif environment. Despite this, if you wish it can be preserved in text using write_motifs().

A note on motif size

The number of rows for each k-let matrix is n^k, with n being the number of letters in the alphabet being used. This means that the size of the k-let matrix can become quite large as k increases. For example, if one were to wish to represent a DNA motif of length 10 as a 10-let, this would require a matrix with 1,048,576 rows (though at this point if what you want is to search for exact sequence matches, the motif format itself is not very useful).

Value

A universalmotif object with filled multifreq slot. The bkg slot is also expanded with corresponding higher order probabilities if add.bkg = TRUE.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

sequences <- create_sequences(seqlen = 10)
motif <- create_motif()
motif.trained <- add_multifreq(motif, sequences, add.k = 2:4)
## peek at the 2-let matrix:
motif.trained["multifreq"]$`2`

sequences <- create_sequences(seqlen = 10)
motif <- create_motif()
motif.trained <- add_multifreq(motif, sequences, add.k = 2:4)
## peek at the 2-let matrix:
motif.trained["multifreq"]$`2`

Arabidopsis motif in `universalmotif` format.

Description

Arabidopsis motif trained from ArabidopsisPromoters using MEME version 4. This motif was generated at the command line using the following command: ⁠meme promoters.fa -revcomp -nmotifs 3 -mod anr -dna⁠.

Usage

ArabidopsisMotif
ArabidopsisMotif

Format

universalmotif

Arabidopsis promoters as a `DNAStringSet`.

Description

50 Arabidopsis promoters, each 1000 bases long. See the "Sequence manipulation and scanning" vignette for an example workflow describing extracting promoter sequences.

Usage

ArabidopsisPromoters
ArabidopsisPromoters

Format

DNAStringSet

Compare motifs.

Description

Compare motifs using one of the several available metrics. See the "Motif comparisons and P-values" vignette for detailed information.

Usage

compare_motifs(motifs, compare.to, db.scores, use.freq = 1,
  use.type = "PPM", method = "PCC", tryRC = TRUE, min.overlap = 6,
  min.mean.ic = 0.25, min.position.ic = 0, relative_entropy = FALSE,
  normalise.scores = FALSE, max.p = 0.01, max.e = 10, nthreads = 1,
  score.strat = "a.mean", output.report, output.report.max.print = 10)
compare_motifs(motifs, compare.to, db.scores, use.freq = 1,
  use.type = "PPM", method = "PCC", tryRC = TRUE, min.overlap = 6,
  min.mean.ic = 0.25, min.position.ic = 0, relative_entropy = FALSE,
  normalise.scores = FALSE, max.p = 0.01, max.e = 10, nthreads = 1,
  score.strat = "a.mean", output.report, output.report.max.print = 10)

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`compare.to`	`numeric` If missing, compares all motifs to all other motifs. Otherwise compares all motifs to the specified motif(s).
`db.scores`	`data.frame` or `DataFrame`. See `details`.
`use.freq`	`numeric(1)`. For comparing the `multifreq` slot.
`use.type`	`character(1)` One of `'PPM'` and `'ICM'`. The latter allows for taking into account the background frequencies if `relative_entropy = TRUE`. Note that `'ICM'` is not allowed when `method = c("ALLR", "ALLR_LL")`.
`method`	`character(1)` One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`max.p`	`numeric(1)` Maximum P-value allowed in reporting matches. Only used if `compare.to` is set.
`max.e`	`numeric(1)` Maximum E-value allowed in reporting matches. Only used if `compare.to` is set. The E-value is the P-value multiplied by the number of input motifs times two.
`nthreads`	`numeric(1)` Run `compare_motifs()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
`output.report`	`character(1)` Provide a filename for `compare_motifs()` to write an html ouput report to. The top matches are shown alongside figures of the match alignments. This requires the `knitr` and `rmarkdown` packages. (Note: still in development.)
`output.report.max.print`	`numeric(1)` Maximum number of top matches to print.

Details

Available metrics

The following metrics are available:

Euclidean distance (EUCL) (Choi et al. 2004)
Weighted Euclidean distance (WEUCL)
Kullback-Leibler divergence (KL) (Kullback and Leibler 1951; Roepcke et al. 2005)
Hellinger distance (HELL) (Hellinger 1909)
Squared Euclidean distance (SEUCL)
Manhattan distance (MAN)
Pearson correlation coefficient (PCC)
Weighted Pearson correlation coefficient (WPCC)
Sandelin-Wasserman similarity (SW), or sum of squared distances (Sandelin and Wasserman 2004)
Average log-likelihood ratio (ALLR) (Wang and Stormo 2003)
Lower limit ALLR (ALLR_LL) (Mahony et al. 2007)
Bhattacharyya coefficient (BHAT) (Bhattacharyya 1943)

Comparisons are calculated between two motifs at a time. All possible alignments are scored, and the best score is reported. In an alignment scores are calculated individually between columns. How those scores are combined to generate the final alignment scores depends on score.strat.

See the "Motif comparisons and P-values" vignette for a description of the various metrics. Note that PCC, WPCC, SW, ALLR, ALLR_LL and BHAT are similarities; higher values mean more similar motifs. For the remaining metrics, values closer to zero represent more similar motifs.

Small pseudocounts are automatically added when one of the following methods is used: KL, ALLR, ALLR_LL, IS. This is avoid zeros in the calculations.

Calculating P-values

To note regarding p-values: P-values are pre-computed using the make_DBscores() function. If not given, then uses a set of internal precomputed P-values from the JASPAR2018 CORE motifs. These precalculated scores are dependent on the length of the motifs being compared. This takes into account that comparing small motifs with larger motifs leads to higher scores, since the probability of finding a higher scoring alignment is higher.

The default P-values have been precalculated for regular DNA motifs. They are of little use for motifs with a different number of alphabet letters (or even the multifreq slot).

Value

matrix if compare.to is missing; DataFrame otherwise. For the latter, function args are stored in the metadata slot.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Bhattacharyya A (1943). “On a measure of divergence between two statistical populations defined by their probability distributions.” Bulletin of the Calcutta Mathematical Society, 35, 99-109.

Choi I, Kwon J, Kim S (2004). “Local feature frequency profile: a method to measure structural similarity in proteins.” PNAS, 101, 3797-3802.

Hellinger E (1909). “Neue Begrundung der Theorie quadratischer Formen von unendlichvielen Veranderlichen.” Journal fur die reine und angewandte Mathematik, 136, 210-271.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Cheneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A (2018). “JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.” Nucleic Acids Research, 46, D260-D266.

Kullback S, Leibler RA (1951). “On information and sufficiency.” The Annals of Mathematical Statistics, 22, 79-86.

Itakura F, Saito S (1968). “Analysis synthesis telephony based on the maximum likelihood method.” In 6th International Congress on Acoustics, C-17.

Mahony S, Auron PE, Benos PV (2007). “DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies.” PLoS Computational Biology, 3.

Pietrokovski S (1996). “Searching databases of conserved sequence regions by aligning protein multiple-alignments.” Nucleic Acids Research, 24, 3836-3845.

Roepcke S, Grossmann S, Rahmann S, Vingron M (2005). “T-Reg Comparator: an analysis tool for the comparison of position weight matrices.” Nucleic Acids Research, 33, W438-W441.

Sandelin A, Wasserman WW (2004). “Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics.” Journal of Molecular Biology, 338, 207-215.

Wang T, Stormo GD (2003). “Combining phylogenetic data with co-regulated genes to identify motifs.” Bioinformatics, 19, 2369-2380.

Examples

motif1 <- create_motif(name = "1")
motif2 <- create_motif(name = "2")
motif1vs2 <- compare_motifs(c(motif1, motif2), method = "PCC")
## To get a dist object:
as.dist(1 - motif1vs2)

motif3 <- create_motif(name = "3")
motif4 <- create_motif(name = "4")
motifs <- c(motif1, motif2, motif3, motif4)
## Compare motif "2" to all the other motifs:
if (R.Version()$arch != "i386") {
compare_motifs(motifs, compare.to = 2, max.p = 1, max.e = Inf)
}

## If you are working with a large list of motifs and the mean.min.ic
## option is not set to zero, you may get a number of failed comparisons
## due to low IC. To filter the list of motifs to avoid these, use
## the average_ic() function to remove motifs with low average IC:
## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb)[1:100]
compare_motifs(motifs)
#> Warning in compare_motifs(motifs) :
#>   Some comparisons failed due to low IC
motifs <- motifs[average_ic(motifs) > 0.5]
compare_motifs(motifs)

## End(Not run)


motif1 <- create_motif(name = "1")
motif2 <- create_motif(name = "2")
motif1vs2 <- compare_motifs(c(motif1, motif2), method = "PCC")
## To get a dist object:
as.dist(1 - motif1vs2)

motif3 <- create_motif(name = "3")
motif4 <- create_motif(name = "4")
motifs <- c(motif1, motif2, motif3, motif4)
## Compare motif "2" to all the other motifs:
if (R.Version()$arch != "i386") {
compare_motifs(motifs, compare.to = 2, max.p = 1, max.e = Inf)
}

## If you are working with a large list of motifs and the mean.min.ic
## option is not set to zero, you may get a number of failed comparisons
## due to low IC. To filter the list of motifs to avoid these, use
## the average_ic() function to remove motifs with low average IC:
## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb)[1:100]
compare_motifs(motifs)
#> Warning in compare_motifs(motifs) :
#>   Some comparisons failed due to low IC
motifs <- motifs[average_ic(motifs) > 0.5]
compare_motifs(motifs)

## End(Not run)

Convert motif class.

Description

Allows for easy transfer of motif information between different classes as defined by other Bioconductor packages. This function is also used by nearly all other functions in this package, so any motifs of a compatible class can be used without needing to be converted beforehand.

Usage

convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'AsIs'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'list'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'universalmotif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'MotifList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'TFFMFirst'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PFMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'ICMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'XMatrixList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pwm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pcm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pfm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWM'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'Motif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'matrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'AsIs'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'list'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'universalmotif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'MotifList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'TFFMFirst'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PFMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'ICMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'XMatrixList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pwm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pcm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pfm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWM'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'Motif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'matrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

Arguments

`motifs`	Single motif object or list. See details.
`class`	`character(1)` Desired motif class. Input as 'package-class'. If left empty, defaults to 'universalmotif-universalmotif'. (See details.)

Details

Input

The following packge-class combinations can be used as input:

MotifDb-MotifList
TFBSTools-PFMatrix
TFBSTools-PWMatrix
TFBSTools-ICMatrix
TFBSTools-PFMatrixList
TFBSTools-PWMatrixList
TFBSTools-ICMatrixList
TFBSTools-TFFMFirst
seqLogo-pwm
motifStack-pcm
motifStack-pfm
PWMEnrich-PWM
motifRG-Motif
universalmotif-universalmotif
matrix

Output

The following package-class combinations can be output:

MotifDb-MotifList
TFBSTools-PFMatrix
TFBSTools-PWMatrix
TFBSTools-ICMatrix
TFBSTools-TFFMFirst
seqLogo-pwm
motifStack-pcm
motifStack-pfm
PWMEnrich-PWM
Biostrings-PWM (type = 'log2prob')
rGADEM-motif
universalmotif-universalmotif (the default, no need to specify this)

Note: MotifDb-MotifList output was a later addition to convert_motifs(). As a result, to stay consistent with previous behaviour most functions will always convert MotifDb-MotifList objects to a list of universalmotif motifs, even if other formats would be simply returned as is (e.g. for other formats, filter_motifs() will return the input format; for MotifDb-MotifList, a list of universalmotif objects will be returned).

Value

Single motif object or list.

Methods (by class)

AsIs: Generate an error to remind users to run to_list() instead of using the column from to_df() directly.
list: Convert a list of motifs.
universalmotif: Convert a universalmotif object.
MotifList: Convert MotifList motifs. (MotifDb)
TFFMFirst: Convert TFFMFirst motifs. (TFBSTools)
PFMatrix: Convert PFMatrix motifs. (TFBSTools)
PWMatrix: Convert PWMatrix motifs. (TFBSTools)
ICMatrix: Convert ICMatrix motifs. (TFBSTools)
XMatrixList: Convert XMatrixList motifs. (TFBSTools)
pwm: Convert pwm motifs. (seqLogo)
pcm: Convert pcm motifs. (motifStack)
pfm: Convert pfm motifs. (motifStack)
PWM: Convert PWM motifs. (PWMEnrich)
Motif: Convert Motif motifs. (motifRG)
matrix: Create motif from matrices.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Bembom O (2018). seqLogo: Sequence logos for DNA sequence alignments. R package version 1.46.0.

Droit A, Gottardo R, Robertson G, Li L (2014). rGADEM: de novo motif discovery. R package version 2.28.0.

Mercier E, Gottardo R (2014). MotIV: Motif Identification and Validation. R package version 1.36.0.

Ou J, Wolfe SA, Brodsky MH, Zhu LJ (2018). “motifStack for the analysis of transcription factor binding site evolution.” Nature Methods, 15, 8-9. doi: 10.1038/nmeth.4555.

Shannon P, Richards M (2018). MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs. R package version 1.22.0.

Stojnic R, Diez D (2015). PWMEnrich: PWM enrichment analysis. R package version 4.16.0.

Tan G, Lenhard B (2016). “TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.” Bioinformatics, 32, 1555-1556. doi: 10.1093/bioinformatics/btw024.

Yao Z (2012). motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset. R package version 1.24.0.

Examples

# Convert from universalmotif:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
if (requireNamespace("motifStack", quietly = TRUE)) {
  jaspar.motifstack.pfm <- convert_motifs(jaspar, "motifStack-pfm")
}

# Convert from another class to universalmotif:
if (requireNamespace("TFBSTools", quietly = TRUE)) {
library(TFBSTools)
data(MA0003.2)
motif <- convert_motifs(MA0003.2)

# Convert from another class to another class
if (requireNamespace("PWMEnrich", quietly = TRUE)) {
  motif <- convert_motifs(MA0003.2, "PWMEnrich-PWM")
}

# The 'convert_motifs' function is embedded in the rest of the universalmotif
# functions: non-universalmotif class motifs can be used
MA0003.2.trimmed <- trim_motifs(MA0003.2)
# Note: if the motif object going in has information that the
# 'universalmotif' class can't hold, it will be lost
}

# Convert from universalmotif:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
if (requireNamespace("motifStack", quietly = TRUE)) {
  jaspar.motifstack.pfm <- convert_motifs(jaspar, "motifStack-pfm")
}

# Convert from another class to universalmotif:
if (requireNamespace("TFBSTools", quietly = TRUE)) {
library(TFBSTools)
data(MA0003.2)
motif <- convert_motifs(MA0003.2)

# Convert from another class to another class
if (requireNamespace("PWMEnrich", quietly = TRUE)) {
  motif <- convert_motifs(MA0003.2, "PWMEnrich-PWM")
}

# The 'convert_motifs' function is embedded in the rest of the universalmotif
# functions: non-universalmotif class motifs can be used
MA0003.2.trimmed <- trim_motifs(MA0003.2)
# Note: if the motif object going in has information that the
# 'universalmotif' class can't hold, it will be lost
}

Convert universalmotif type.

Description

Switch between position count matrix (PCM), position probability matrix (PPM), position weight matrix (PWM), and information count matrix (ICM) types. See the "Introduction to sequence motifs" vignette for details. Please also note that type conversion occurs implicitly throughout the universalmotif package, so there is generally no need to perform this manual conversion. Also please be aware that the message concerning pseudocount-adjusting motifs can be disabled via options(pseudocount.warning=FALSE).

Usage

convert_type(motifs, type, pseudocount, nsize_correction = FALSE,
  relative_entropy = FALSE)
convert_type(motifs, type, pseudocount, nsize_correction = FALSE,
  relative_entropy = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`pseudocount`	`numeric(1)` Correction to be applied to prevent `-Inf` from appearing in PWM matrices. If missing, the pseudocount stored in the universalmotif 'pseudocount' slot will be used.
`nsize_correction`	`logical(1)` If true, the ICM at each position will be corrected to account for small sample sizes. Only used if `relative_entropy = FALSE`.
`relative_entropy`	`logical(1)` If true, the ICM will be calculated as relative entropy. See details.

Details

PCM

Position count matrix (PCM), also known as position frequency matrix (PFM). For n sequences from which the motif was built, each position is represented by the numbers of each letter at that position. In theory all positions should have sums equal to n, but not all databases are this consistent. If converting from another type to PCM, column sums will be equal to the 'nsites' slot. If empty, 100 is used.

PPM

Position probability matrix (PPM), also known as position frequency matrix (PFM). At each position, the probability of individual letters is calculated by dividing the count for that letter by the total sum of counts at that position (letter_count / position_total). As a result, each position will sum to 1. Letters with counts of 0 will thus have a probability of 0, which can be undesirable when searching for motifs in a set of sequences. To avoid this a pseudocount can be added ((letter_count + pseudocount) / (position_total + pseudocount)).

PWM

Position weight matrix (PWM; Stormo et al. (1982)), also known as position-specific weight matrix (PSWM), position-specific scoring matrix (PSSM), or log-odds matrix. At each position, each letter is represented by it's log-likelihood (log2(letter_probability / background_probility)), which is normalized using the background letter frequencies. A PWM matrix is constructed from a PPM. If any position has 0-probability letters to which pseudocounts were not added, then the final log-likelihood of these letters will be -Inf.

ICM

Information content matrix (ICM; Schneider and Stephens 1990). An ICM is a PPM where each letter probability is multiplied by the total information content at that position. The information content of each position is determined as: totalIC - Hi, where the total information totalIC

totalIC <- log2(alphabet_length), and the Shannon entropy (Shannon 1948) for a specific position (Hi)

⁠Hi <- -sum(sapply(alphabet_frequencies, function(x) x * log(2))⁠.

As a result, the total sum or height of each position is representative of it's sequence conservation, measured in the unit 'bits', which is a unit of energy (Schneider 1991; see https://fr-s-schneider.ncifcrf.gov/logorecommendations.html for more information). However not all programs will calculate information content the same. Some will 'correct' the total information content at each position using a correction factor as described by Schneider et al. (1986). This correction can applied by setting nsize_correction = TRUE, however it will only be applied if the 'nsites' slot is not empty. This is done using TFBSTools:::schneider_correction (Tan and Lenhard 2016). As such, converting from an ICM to which some form of correction has been applied will result in a PCM/PPM/PWM with slight inaccuracies.

Another method of calculating information content is calculating the relative entropy, also known as Kullback-Leibler divergence (Kullback and Leibler 1951). This accounts for background frequencies, which can be useful for genomes with a heavy imbalance in letter frequencies. For each position, the individual letter frequencies are calculated as letter_freq * log2(letter_freq / bkg_freq). When calculating information content using Shannon entropy, the maximum content for each position will always be log2(alphabet_length). This does not hold for information content calculated as relative entropy. Please note that conversion from ICM assumes the information content was not calculated as relative entropy.

Value

See convert_motifs() for possible output motif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Kullback S, Leibler RA (1951). “On information and sufficiency.” The Annals of Mathematical Statistics, 22, 79-86.

Nishida K, Frith MC, Nakai K (2009). “Pseudocounts for transcription factor binding sites.” Nucleic Acids Research, 37, 939-944.

Schneider TD, Stormo GD, Gold L, Ehrenfeucht A (1986). “Information content of binding sites on nucleotide sequences.” Journal of Molecular Biology, 188, 415-431.

Schneider TD, Stephens RM (1990). “Sequence Logos: A New Way to Display Consensus Sequences.” Nucleic Acids Research, 18, 6097-6100.

Schneider TD (1991). “Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines.” Journal of Theoretical Biology, 148, 125-137.

Shannon CE (1948). “A Mathematical Theory of Communication.” Bell System Technical Journal, 27, 379-423.

Stormo GD, Schneider TD, Gold L, Ehrenfeucht A (1982). “Use of the Perceptron algorithm to distinguish translational initiation sites in E. coli.” Nucleic Acids Research, 10, 2997-3011.

Tan G, Lenhard B (2016). “TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.” Bioinformatics, 32, 1555-1556. doi: 10.1093/bioinformatics/btw024.

Examples

jaspar.pcm <- read_jaspar(system.file("extdata", "jaspar.txt",
                                      package = "universalmotif"))

## The motifs pseudocounts are 1: these will be used in the PCM->PPM
## calculation
jaspar.pwm <- convert_type(jaspar.pcm, type = "PPM")

## Setting pseudocount to 0 will prevent any correction from being
## applied to PPM/PWM matrices, overriding the motifs own pseudocounts
jaspar.pwm <- convert_type(jaspar.pcm, type = "PWM", pseudocount = 0)

jaspar.pcm <- read_jaspar(system.file("extdata", "jaspar.txt",
                                      package = "universalmotif"))

## The motifs pseudocounts are 1: these will be used in the PCM->PPM
## calculation
jaspar.pwm <- convert_type(jaspar.pcm, type = "PPM")

## Setting pseudocount to 0 will prevent any correction from being
## applied to PPM/PWM matrices, overriding the motifs own pseudocounts
jaspar.pwm <- convert_type(jaspar.pcm, type = "PWM", pseudocount = 0)

Create a motif.

Description

Create a motif from a set of sequences, a matrix, or generate a random motif. See the "Motif import, export and manipulation" vignette for details.

Usage

create_motif(input, alphabet, type = "PPM", name = "motif",
  pseudocount = 0, bkg, nsites, altname, family, organism, bkgsites, strand,
  pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'missing'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'numeric'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'character'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'matrix'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'DNAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'RNAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'AAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'BStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)
create_motif(input, alphabet, type = "PPM", name = "motif",
  pseudocount = 0, bkg, nsites, altname, family, organism, bkgsites, strand,
  pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'missing'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'numeric'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'character'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'matrix'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'DNAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'RNAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'AAStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

## S4 method for signature 'BStringSet'
create_motif(input, alphabet, type = "PPM",
  name = "motif", pseudocount = 0, bkg, nsites, altname, family, organism,
  bkgsites, strand, pval, qval, eval, extrainfo, add.multifreq)

Arguments

`input`	`character`, `numeric`, `matrix`, `XStringSet`, or `missing`.
`alphabet`	`character(1)` One of `c('DNA', 'RNA', 'AA')`, or a combined string representing the letters. If no alphabet is provided then it will try and guess the alphabet from the input.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`name`	`character(1)` Motif name.
`pseudocount`	`numeric(1)` Correction to be applied to prevent `-Inf` from appearing in PWM matrices. Defaults to 0.
`bkg`	`numeric` A vector of probabilities, each between 0 and 1. If higher order backgrounds are provided, then the elements of the vector must be named. If unnamed, then the order of probabilities must be in the same order as the alphabetically sorted sequence alphabet.
`nsites`	`numeric(1)` Number of sites the motif was constructed from. If blank, then `create_motif()` will guess the appropriate number if possible. To prevent this, provide `nsites = numeric()`.
`altname`	`character(1)` Alternate motif name.
`family`	`character(1)` Transcription factor family.
`organism`	`character(1)` Species of origin.
`bkgsites`	`numeric(1)` Total number of sites used to find the motif.
`strand`	`character(1)` Whether the motif is specific to a certain strand. Acceptable strands are '+', '-', and '+-' (to represent both strands). Note that '-+' and '*' can also be provided to represent both strands, but the final strand in the `universalmotif` object will be set to '+-'.
`pval`	`numeric(1)` P-value associated with motif.
`qval`	`numeric(1)` Adjusted P-value associated with motif.
`eval`	`numeric(1)` E-value associated with motif.
`extrainfo`	`character` Any other extra information, represented as a named character vector.
`add.multifreq`	`numeric` If the motif is created from a set of sequences, then the `add_multifreq()` function can be run at the same time (with `RC = FALSE`).

Details

The aim of this function is provide an easy interface to creating universalmotif motifs, as an alternative to the default class constructor (i.e. new('universalmotif', name=...)). See examples for potential use cases.

Note: when generating random motifs, the nsites slot is also given a random value.

See the examples section for more info on motif creation.

Value

universalmotif object.

Methods (by class)

missing: Create a random motif of length 10.
numeric: Create a random motif with a specified length.
character: Create motif from a consensus string.
matrix: Create motif from a matrix.
DNAStringSet: Create motif from a DNAStringSet.
RNAStringSet: Create motif from a RNAStringSet.
AAStringSet: Create motif from a AAStringSet.
BStringSet: Create motif from a BStringSet.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

##### create motifs from a single string

# Motif is by default generated as a PPM: change final type as desired
DNA.motif <- create_motif("TATAWAW")
DNA.motif <- create_motif("TATAWAW", type = "PCM")

# Nsites will be set to the number of input sequences unless specified or
# a single string is used as input
DNA.motif <- create_motif("TTTTTTT", nsites = 10)

# Ambiguity letters can be used:
DNA.motif <- create_motif("TATAWAW")
DNA.motif <- create_motif("NNVVWWAAWWDDN")

# Be careful about setting nsites when using ambiguity letters!
DNA.motif <- create_motif("NNVVWWAAWWDDN", nsites = 1)

RNA.motif <- create_motif("UUUCCG")

# 'create_motif' will try to detect the alphabet type; this can be
# unreliable for AA and custom alphabets as DNA and RNA alphabets are
# detected first
AA.motif <- create_motif("AVLK", alphabet = "AA")

custom.motif <- create_motif("QWER", alphabet = "QWER")
# Specify custom alphabet
custom.motif <- create_motif("QWER", alphabet = "QWERASDF")

###### Create motifs from multiple strings of equal length

DNA.motif <- create_motif(c("TTTT", "AAAA", "AACC", "TTGG"), type = "PPM")
DNA.motif <- create_motif(c("TTTT", "AAAA", "AACC", "TTGG"), nsites = 20)
RNA.motif <- create_motif(c("UUUU", "AAAA", "AACC", "UUGG"), type = "PWM")
AA.motif <- create_motif(c("ARNDCQ", "EGHILK", "ARNDCQ"), alphabet = "AA")
custom.motif <- create_motif(c("POIU", "LKJH", "POIU", "CVBN"),
                             alphabet = "POIULKJHCVBN")

# Ambiguity letters are only allowed for single consensus strings: the
# following fails
## Not run: 
create_motif(c("WWTT", "CCGG"))
create_motif(c("XXXX", "XXXX"), alphabet = "AA")

## End(Not run)

##### Create motifs from XStringSet objects

library(Biostrings)

DNA.set <- DNAStringSet(c("TTTT", "AAAA", "AACC", "TTGG"))
DNA.motif <- create_motif(DNA.set)
RNA.set <- RNAStringSet(c("UUUU", "AACC", "UUCC"))
RNA.motif <- create_motif(RNA.set)
AA.set <- AAStringSet(c("VVVLLL", "AAAIII"))
AA.motif <- create_motif(AA.set)

# Custom motifs can be created from BStringSet objects
B.set <- BStringSet(c("QWER", "ASDF", "ZXCV", "TYUI"))
custom.motif <- create_motif(B.set)

##### Create motifs with filled 'multifreq' slot

DNA.motif.k2 <- create_motif(DNA.set, add.multifreq = 2)

##### Create motifs from matrices

mat <- matrix(c(1, 1, 1, 1,
                2, 0, 2, 0,
                0, 2, 0, 2,
                0, 0, 0, 0),
                nrow = 4, byrow = TRUE)
DNA.motif <- create_motif(mat, alphabet = "DNA")
RNA.motif <- create_motif(mat, alphabet = "RNA", nsites = 20)
custom.motif <- create_motif(mat, alphabet = "QWER")

# Specify custom alphabet
custom.motif <- create_motif(mat, alphabet = "QWER")

# Alphabet can be detected from rownames
rownames(mat) <- DNA_BASES
DNA.motif <- create_motif(mat)
rownames(mat) <- c("Q", "W", "E", "R")
custom.motif <- create_motif(mat)

# Matrices can also be used as input
mat.ppm <- matrix(c(0.1, 0.1, 0.1, 0.1,
                    0.5, 0.5, 0.5, 0.5,
                    0.1, 0.1, 0.1, 0.1,
                    0.3, 0.3, 0.3, 0.3),
                    nrow = 4, byrow = TRUE)

DNA.motif <- create_motif(mat.ppm, alphabet = "DNA", type = "PPM")

##### Create random motifs

# These are generated as PPMs with 10 positions

DNA.motif <- create_motif()
RNA.motif <- create_motif(alphabet = "RNA")
AA.motif <- create_motif(alphabet = "AA")
custom.motif <- create_motif(alphabet = "QWER")

# The number of positions can be specified

DNA.motif <- create_motif(5)

# If the background frequencies are not provided, they are generated
# using `rpois`; positions are created using `rdirichlet(1, bkg)`.
# (calling `create_motif()` creates motifs with an average
# positional IC of 1)

DNA.motif <- create_motif(bkg = c(0.3, 0.2, 0.2, 0.3))
DNA.motif <- create_motif(10, bkg = c(0.1, 0.4, 0.4, 0.1))

##### create motifs from a single string

# Motif is by default generated as a PPM: change final type as desired
DNA.motif <- create_motif("TATAWAW")
DNA.motif <- create_motif("TATAWAW", type = "PCM")

# Nsites will be set to the number of input sequences unless specified or
# a single string is used as input
DNA.motif <- create_motif("TTTTTTT", nsites = 10)

# Ambiguity letters can be used:
DNA.motif <- create_motif("TATAWAW")
DNA.motif <- create_motif("NNVVWWAAWWDDN")

# Be careful about setting nsites when using ambiguity letters!
DNA.motif <- create_motif("NNVVWWAAWWDDN", nsites = 1)

RNA.motif <- create_motif("UUUCCG")

# 'create_motif' will try to detect the alphabet type; this can be
# unreliable for AA and custom alphabets as DNA and RNA alphabets are
# detected first
AA.motif <- create_motif("AVLK", alphabet = "AA")

custom.motif <- create_motif("QWER", alphabet = "QWER")
# Specify custom alphabet
custom.motif <- create_motif("QWER", alphabet = "QWERASDF")

###### Create motifs from multiple strings of equal length

DNA.motif <- create_motif(c("TTTT", "AAAA", "AACC", "TTGG"), type = "PPM")
DNA.motif <- create_motif(c("TTTT", "AAAA", "AACC", "TTGG"), nsites = 20)
RNA.motif <- create_motif(c("UUUU", "AAAA", "AACC", "UUGG"), type = "PWM")
AA.motif <- create_motif(c("ARNDCQ", "EGHILK", "ARNDCQ"), alphabet = "AA")
custom.motif <- create_motif(c("POIU", "LKJH", "POIU", "CVBN"),
                             alphabet = "POIULKJHCVBN")

# Ambiguity letters are only allowed for single consensus strings: the
# following fails
## Not run: 
create_motif(c("WWTT", "CCGG"))
create_motif(c("XXXX", "XXXX"), alphabet = "AA")

## End(Not run)

##### Create motifs from XStringSet objects

library(Biostrings)

DNA.set <- DNAStringSet(c("TTTT", "AAAA", "AACC", "TTGG"))
DNA.motif <- create_motif(DNA.set)
RNA.set <- RNAStringSet(c("UUUU", "AACC", "UUCC"))
RNA.motif <- create_motif(RNA.set)
AA.set <- AAStringSet(c("VVVLLL", "AAAIII"))
AA.motif <- create_motif(AA.set)

# Custom motifs can be created from BStringSet objects
B.set <- BStringSet(c("QWER", "ASDF", "ZXCV", "TYUI"))
custom.motif <- create_motif(B.set)

##### Create motifs with filled 'multifreq' slot

DNA.motif.k2 <- create_motif(DNA.set, add.multifreq = 2)

##### Create motifs from matrices

mat <- matrix(c(1, 1, 1, 1,
                2, 0, 2, 0,
                0, 2, 0, 2,
                0, 0, 0, 0),
                nrow = 4, byrow = TRUE)
DNA.motif <- create_motif(mat, alphabet = "DNA")
RNA.motif <- create_motif(mat, alphabet = "RNA", nsites = 20)
custom.motif <- create_motif(mat, alphabet = "QWER")

# Specify custom alphabet
custom.motif <- create_motif(mat, alphabet = "QWER")

# Alphabet can be detected from rownames
rownames(mat) <- DNA_BASES
DNA.motif <- create_motif(mat)
rownames(mat) <- c("Q", "W", "E", "R")
custom.motif <- create_motif(mat)

# Matrices can also be used as input
mat.ppm <- matrix(c(0.1, 0.1, 0.1, 0.1,
                    0.5, 0.5, 0.5, 0.5,
                    0.1, 0.1, 0.1, 0.1,
                    0.3, 0.3, 0.3, 0.3),
                    nrow = 4, byrow = TRUE)

DNA.motif <- create_motif(mat.ppm, alphabet = "DNA", type = "PPM")

##### Create random motifs

# These are generated as PPMs with 10 positions

DNA.motif <- create_motif()
RNA.motif <- create_motif(alphabet = "RNA")
AA.motif <- create_motif(alphabet = "AA")
custom.motif <- create_motif(alphabet = "QWER")

# The number of positions can be specified

DNA.motif <- create_motif(5)

# If the background frequencies are not provided, they are generated
# using `rpois`; positions are created using `rdirichlet(1, bkg)`.
# (calling `create_motif()` creates motifs with an average
# positional IC of 1)

DNA.motif <- create_motif(bkg = c(0.3, 0.2, 0.2, 0.3))
DNA.motif <- create_motif(10, bkg = c(0.1, 0.4, 0.4, 0.1))

Create random sequences.

Description

Generate random sequences from any set of characters, represented as XStringSet objects.

Usage

create_sequences(alphabet = "DNA", seqnum = 100, seqlen = 100, freqs,
  nthreads = 1, rng.seed = sample.int(10000, 1))
create_sequences(alphabet = "DNA", seqnum = 100, seqlen = 100, freqs,
  nthreads = 1, rng.seed = sample.int(10000, 1))

Arguments

`alphabet`	`character(1)` One of `c('DNA', 'RNA', 'AA')`, or a string of characters to be used as the alphabet.
`seqnum`	`numeric(1)` Number of sequences to generate.
`seqlen`	`numeric(1)` Length of random sequences.
`freqs`	`numeric` A named vector of probabilities. The length of the vector must be the power of the number of letters in the sequence alphabet. Probabilities can only be provided for a single size k.
`nthreads`	`numeric(1)` Run `create_sequences()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with `seqnum = 1`.
`rng.seed`	`numeric(1)` Set random number generator seed. Since sequence creation can occur simultaneously in multiple threads using C++, it cannot communicate with the regular `R` random number generator state and thus requires an independent seed. Each individual sequence creation instance is given the following seed: `rng.seed * index`. The default is to pick a random number as chosen by `sample()`, which effectively is making `create_sequences()` dependent on the R RNG state.

Value

XStringSet The returned sequences are unnamed.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Create DNA sequences with slightly increased AT content:
sequences <- create_sequences(freqs = c(A=0.3, C=0.2, G=0.2, T=0.3))
## Create custom sequences:
sequences.QWER <- create_sequences("QWER")
## You can include non-alphabet characters are well, even spaces:
sequences.custom <- create_sequences("!@#$ ")

## Create DNA sequences with slightly increased AT content:
sequences <- create_sequences(freqs = c(A=0.3, C=0.2, G=0.2, T=0.3))
## Create custom sequences:
sequences.QWER <- create_sequences("QWER")
## You can include non-alphabet characters are well, even spaces:
sequences.custom <- create_sequences("!@#$ ")

Enrich for input motifs in a set of sequences.

Description

Given a set of target and background sequences, test if the input motifs are significantly enriched in the targets sequences relative to the background sequences. See the "Sequence manipulation and scanning" vignette.

Usage

enrich_motifs(motifs, sequences, bkg.sequences, max.p = 0.001,
  max.q = 0.001, max.e = 0.001, qval.method = "fdr", threshold = 1e-04,
  threshold.type = "pvalue", verbose = 0, RC = TRUE, use.freq = 1,
  shuffle.k = 2, shuffle.method = "euler", return.scan.results = FALSE,
  nthreads = 1, rng.seed = sample.int(10000, 1), motif_pvalue.k = 8,
  use.gaps = TRUE, allow.nonfinite = FALSE, warn.NA = TRUE,
  no.overlaps = TRUE, no.overlaps.by.strand = FALSE,
  no.overlaps.strat = "score", respect.strand = FALSE,
  motif_pvalue.method = c("dynamic", "exhaustive"),
  scan_sequences.qvals.method = c("BH", "fdr", "bonferroni"),
  mode = c("total.hits", "seq.hits"), pseudocount = 1)
enrich_motifs(motifs, sequences, bkg.sequences, max.p = 0.001,
  max.q = 0.001, max.e = 0.001, qval.method = "fdr", threshold = 1e-04,
  threshold.type = "pvalue", verbose = 0, RC = TRUE, use.freq = 1,
  shuffle.k = 2, shuffle.method = "euler", return.scan.results = FALSE,
  nthreads = 1, rng.seed = sample.int(10000, 1), motif_pvalue.k = 8,
  use.gaps = TRUE, allow.nonfinite = FALSE, warn.NA = TRUE,
  no.overlaps = TRUE, no.overlaps.by.strand = FALSE,
  no.overlaps.strat = "score", respect.strand = FALSE,
  motif_pvalue.method = c("dynamic", "exhaustive"),
  scan_sequences.qvals.method = c("BH", "fdr", "bonferroni"),
  mode = c("total.hits", "seq.hits"), pseudocount = 1)

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`sequences`	`XStringSet` Sequences to scan. Alphabet should match motif.
`bkg.sequences`	`XStringSet` Optional. If missing, `shuffle_sequences()` is used to create background sequences from the input sequences.
`max.p`	`numeric(1)` P-value threshold.
`max.q`	`numeric(1)` Adjusted P-value threshold. This is only useful if multiple motifs are being enriched for.
`max.e`	`numeric(1)`. The E-value is calculated by multiplying the P-value with the number of input motifs times two (McLeay and Bailey 2010).
`qval.method`	`character(1)` See `stats::p.adjust()`.
`threshold`	`numeric(1)` See details.
`threshold.type`	`character(1)` One of `c('pvalue', 'qvalue', 'logodds', 'logodds.abs')`. See details.
`verbose`	`numeric(1)` 0 for no output, 4 for max verbosity.
`RC`	`logical(1)` If `TRUE`, check reverse complement of the input sequences. Only available for DNA/RNA.
`use.freq`	`numeric(1)` The default, 1, uses the motif matrix (from the `motif['motif']` slot) to search for sequences. If a higher number is used, then the matching k-let matrix from the `motif['multifreq']` slot is used. See `add_multifreq()`.
`shuffle.k`	`numeric(1)` The k-let size to use when shuffling input sequences. Only used if no background sequences are input. See `shuffle_sequences()`.
`shuffle.method`	`character(1)` One of `c('euler', 'markov', 'linear')`. See `shuffle_sequences()`.
`return.scan.results`	`logical(1)` Return output from `scan_sequences()`. For large jobs, leaving this as `FALSE` can save a small amount time by preventing construction of the complete results `data.frame` from `scan_sequences()`.
`nthreads`	`numeric(1)` Run `scan_sequences()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with only a single motif and sequence.
`rng.seed`	`numeric(1)` Set random number generator seed. Since shuffling can occur simultaneously in multiple threads using C++, it cannot communicate with the regular `R` random number generator state and thus requires an independent seed. Each individual sequence in an `XStringSet` object will be given the following seed: `rng.seed * index`. See `shuffle_sequences()`.
`motif_pvalue.k`	`numeric(1)` Control `motif_pvalue()` approximation. See `motif_pvalue()`.
`use.gaps`	`logical(1)` Set this to `FALSE` to ignore motif gaps, if present.
`allow.nonfinite`	`logical(1)` If `FALSE`, then apply a pseudocount if non-finite values are found in the PWM. Note that if the motif has a pseudocount greater than zero and the motif is not currently of type PWM, then this parameter has no effect as the pseudocount will be applied automatically when the motif is converted to a PWM internally. This value is set to `FALSE` by default in order to stay consistent with pre-version 1.8.0 behaviour. A message will be printed if a pseudocount is applied. To disable this, set `options(pseudocount.warning=FALSE)`.
`warn.NA`	`logical(1)` Whether to warn about the presence of non-standard letters in the input sequence, such as those in masked sequences.
`no.overlaps`	`logical(1)` Remove overlapping hits from the same motifs. Overlapping hits from different motifs are preserved. Please note that the current implementation of this feature can add significantly to the run time for large inputs.
`no.overlaps.by.strand`	`logical(1)` Whether to discard overlapping hits from the opposite strand (`TRUE`), or to only discard overlapping hits on the same strand (`FALSE`).
`no.overlaps.strat`	`character(1)` One of `c("score", "order")`. The former option keeps the highest scoring overlapping hit (and the first of these within ties), and the latter simply keeps the first overlapping hit.
`respect.strand`	`logical(1)` If motifs are DNA/RNA, then setting this option to `TRUE` will make `scan_sequences()` only scan the strands of the input sequences as indicated in the motif `strand` slot.
`motif_pvalue.method`	`character(1)` One of `c("dynamic", "exhaustive")`. Algorithm used for calculating P-values. The `"exhaustive"` method involves finding all possible motif matches at or above the specified score using a branch-and-bound algorithm, which can be computationally intensive (Hartman et al., 2013). Additionally, the computation must be repeated for each hit. The `"dynamic"` method calculates the distribution of possible motif scores using a much faster dynamic programming algorithm, and can be recycled for multiple scores (Grant et al., 2011). The only disadvantage is the inability to use `allow.nonfinite = TRUE`. See `motif_pvalue()` for details.
`scan_sequences.qvals.method`	`character(1)` One of `c("fdr", "BH", "bonferroni")`. The method for calculating adjusted P-values for individual motif hits. These are described in depth in the Sequence Searches vignette.
`mode`	`character(1)` One of `c("total.hits", "seq.hits")`. The former enriches for the total count of motif hits across all sequences, whereas the latter only counts motif hits once per sequence (useful for cases where there are many small sequences).
`pseudocount`	`integer(1)` Add a pseudocount to the motif hit counts when performing the Fisher test.

Details

To find enriched motifs, scan_sequences() is run on both target and background sequences. stats::fisher.test() is run to test for enrichment.

See scan_sequences() for more info on scanning parameters.

Value

DataFrame Enrichment results in a DataFrame. Function args and (optionally) scan results are stored in the metadata slot.

Author(s)

Benjamin Jean-Marie Tremblay [email protected]

References

McLeay R, Bailey TL (2010). “Motif Enrichment Analysis: A unified framework and method evaluation.” BMC Bioinformatics, 11.

Examples

data(ArabidopsisPromoters)
data(ArabidopsisMotif)
if (R.Version()$arch != "i386") {
enrich_motifs(ArabidopsisMotif, ArabidopsisPromoters, threshold = 0.01)
}

data(ArabidopsisPromoters)
data(ArabidopsisMotif)
if (R.Version()$arch != "i386") {
enrich_motifs(ArabidopsisMotif, ArabidopsisPromoters, threshold = 0.01)
}

Example motif in `universalmotif` format.

Description

A simple DNA motif. To recreate this motif: create_motif("TATAWAW", nsites = numeric())

Usage

examplemotif
examplemotif

Format

universalmotif

Another example motif in `universalmotif` format.

Description

A simple DNA motif with a non-empty multifreq slot. To recreate to this motif: add_multifreq(examplemotif, DNAStringSet(rep(c("CAAAACC", "CTTTTCC"), 3)))

Usage

examplemotif2
examplemotif2

Format

universalmotif

Filter a list of motifs.

Description

Filter motifs based on the contents of available universalmotif slots. If the input motifs are not of universalmotif, then they will be converted for the duration of the filter_motifs() operation.

Usage

filter_motifs(motifs, name, altname, family, organism, width, alphabet, type,
  icscore, nsites, strand, pval, qval, eval, extrainfo)
filter_motifs(motifs, name, altname, family, organism, width, alphabet, type,
  icscore, nsites, strand, pval, qval, eval, extrainfo)

Arguments

`motifs`	`list` See `convert_motifs()` for acceptable formats.
`name`	`character` Keep motifs by names.
`altname`	`character` Keep motifs by altnames.
`family`	`character` Keep motifs by family.
`organism`	`character` Keep motifs by organism.
`width`	`numeric(1)` Keep motifs with minimum width.
`alphabet`	`character` Keep motifs by alphabet.
`type`	`character` Keep motifs by type.
`icscore`	`numeric(1)` Keep motifs with minimum total IC.
`nsites`	`numeric(1)` Keep motifs with minimum number of target sites.
`strand`	`character` Keeps motifs by strand.
`pval`	`numeric(1)` Keep motifs by max P-value.
`qval`	`numeric(1)` Keep motifs by max Q-value.
`eval`	`numeric(1)` Keep motifs by max E-val.
`extrainfo`	`character` Named character vector of items that must be present in motif `extrainfo` slots.

Value

list Motifs. An attempt will be made to preserve the original class, see convert_motifs() for limitations.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## By minimum IC:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.ic3 <- filter_motifs(jaspar, icscore = 3)

## Starting from version 1.10.0 of the universalmotif package, one
## could instead make use of the universalmotif_df structure:
jaspar.ic3 <- jaspar |> to_df() |> subset(icscore > 3) |> to_list()

## By organism:
## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb)
motifs <- filter_motifs(motifs, organism = c("Athaliana", "Mmusculus"),
                        extrainfo = c("dataSource" = "cisbp_1.02"))
## Or:
motifs <- convert_motifs(MotifDb) |> to_df() |>
  subset(organism %in% c("Athaliana", "Mmusculus") &
    dataSource == "cisbp_1.02") |> to_list()

## End(Not run)

## By minimum IC:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.ic3 <- filter_motifs(jaspar, icscore = 3)

## Starting from version 1.10.0 of the universalmotif package, one
## could instead make use of the universalmotif_df structure:
jaspar.ic3 <- jaspar |> to_df() |> subset(icscore > 3) |> to_list()

## By organism:
## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb)
motifs <- filter_motifs(motifs, organism = c("Athaliana", "Mmusculus"),
                        extrainfo = c("dataSource" = "cisbp_1.02"))
## Or:
motifs <- convert_motifs(MotifDb) |> to_df() |>
  subset(organism %in% c("Athaliana", "Mmusculus") &
    dataSource == "cisbp_1.02") |> to_list()

## End(Not run)

Polygon coordinates for plotting letters.

Description

DataFrame of polygon coordinates used by view_motifs() for plotting letters. It was generated using the createPolygons function from the gglogo package for the font Roboto Medium.

Usage

fontDFroboto
fontDFroboto

Format

DataFrame

Calculate sequence background.

Description

For a set of input sequences, calculate the overall sequence background for any k-let size. For very large sequences DNA and RNA sequences (in the billions of bases), please be aware of the much faster and more efficient Biostrings::oligonucleotideFrequency(). get_bkg() can still be used in these cases, though it may take several seconds or minutes to calculate the results (depending on requested k-let sizes).

Usage

get_bkg(sequences, k = 1:3, as.prob = NULL, pseudocount = 0,
  alphabet = NULL, to.meme = NULL, RC = FALSE, list.out = NULL,
  nthreads = 1, merge.res = TRUE, window = FALSE, window.size = 0.1,
  window.overlap = 0)
get_bkg(sequences, k = 1:3, as.prob = NULL, pseudocount = 0,
  alphabet = NULL, to.meme = NULL, RC = FALSE, list.out = NULL,
  nthreads = 1, merge.res = TRUE, window = FALSE, window.size = 0.1,
  window.overlap = 0)

Arguments

`sequences`	`XStringSet` Input sequences. Note that if multiple sequences are present, the results will be combined into one (unless `merge.res = FALSE`).
`k`	`integer` Size of k-let. Background can be calculated for any k-let size.
`as.prob`	Deprecated.
`pseudocount`	`integer(1)` Add a count to each possible k-let. Prevents any k-let from having 0 or 1 probabilities.
`alphabet`	`character(1)` Provide a custom alphabet to calculate a background for. If `NULL`, then standard letters will be assumed for DNA, RNA and AA sequences, and all unique letters found will be used for `BStringSet` type sequences. Note that letters which are not a part of the standard DNA/RNA/AA alphabets or in the provided alphabet will not be counted in the totals during probability calculations.
`to.meme`	If not `NULL`, then `get_bkg()` will return the sequence background in MEME Markov Background Model format. Input for this argument will be used for `cat(..., file = to.meme)` within `get_bkg()`. See http://meme-suite.org/doc/bfile-format.html for a description of the format.
`RC`	`logical(1)` Calculate the background of the reverse complement of the input sequences as well. Only valid for DNA/RNA.
`list.out`	Deprecated.
`nthreads`	`numeric(1)` Run `get_bkg()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with only a single sequence.
`merge.res`	`logical(1)` Whether to merge results from all sequences or return background data for individual sequences.
`window`	`logical(1)` Determine background in windows.
`window.size`	`numeric` Window size. If a number between 0 and 1 is provided, the value is calculated as the number multiplied by the sequence length.
`window.overlap`	`numeric` Overlap between windows. If a number between 0 and 1 is provided, the value is calculated as the number multiplied by the sequence length.

Value

If to.meme = NULL, a DataFrame with columns klet, count, and probability. If merge.res = FALSE, there will be an additional sequence column. If window = TRUE, there will be an additional start and stop columns.

If to.meme is not NULL, then NULL is returned, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Bailey TL, Elkan C (1994). “Fitting a mixture model by expectation maximization to discover motifs in biopolymers.” Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 2, 28-36.

Examples

## Compare to Biostrings version
library(Biostrings)
seqs.DNA <- create_sequences()
bkg.DNA <- get_bkg(seqs.DNA, k = 3)
bkg.DNA2 <- oligonucleotideFrequency(seqs.DNA, 3, 1, as.prob = FALSE)
bkg.DNA2 <- colSums(bkg.DNA2)
all(bkg.DNA$count == bkg.DNA2)

## Create a MEME background file
get_bkg(seqs.DNA, k = 1:3, to.meme = stdout(), pseudocount = 1)

## Non-DNA/RNA/AA alphabets
seqs.QWERTY <- create_sequences("QWERTY")
bkg.QWERTY <- get_bkg(seqs.QWERTY, k = 1:2)

## Compare to Biostrings version
library(Biostrings)
seqs.DNA <- create_sequences()
bkg.DNA <- get_bkg(seqs.DNA, k = 3)
bkg.DNA2 <- oligonucleotideFrequency(seqs.DNA, 3, 1, as.prob = FALSE)
bkg.DNA2 <- colSums(bkg.DNA2)
all(bkg.DNA$count == bkg.DNA2)

## Create a MEME background file
get_bkg(seqs.DNA, k = 1:3, to.meme = stdout(), pseudocount = 1)

## Non-DNA/RNA/AA alphabets
seqs.QWERTY <- create_sequences("QWERTY")
bkg.QWERTY <- get_bkg(seqs.QWERTY, k = 1:2)

JASPAR2018 CORE database scores

Description

For use with compare_motifs(). The precomputed scores allow for fast P-value estimation. These scores were generated using make_DBscores() with the JASPAR2018 CORE motif set. The scores are organized in a DataFrame. In this DataFrame is the location and scale of scores resulting from a statistical distribution using the the comparisons of JASPAR2018 CORE motifs with randomized motifs of the specified subject and target motif length. Created using make_DBscores() from universalmotif v1.4.0. The parameters used can be seen via S4Vectors::metadata(JASPAR2018_CORE_DBSCORES).

Usage

JASPAR2018_CORE_DBSCORES
JASPAR2018_CORE_DBSCORES

Format

DataFrame with function args in the metadata slot.

Create P-value databases.

Description

Generate data used by compare_motifs() for P-value calculations. By default, compare_motifs() uses an internal database based on the JASPAR2018 core motifs (Khan et al. 2018). Parameters for distributions are are estimated for every combination of motif widths.

Usage

make_DBscores(db.motifs, method = c("PCC", "EUCL", "SW", "KL", "WEUCL",
  "ALLR", "BHAT", "HELL", "WPCC", "SEUCL", "MAN", "ALLR_LL"),
  shuffle.db = TRUE, shuffle.k = 3, shuffle.method = "linear",
  rand.tries = 1000, widths = 5:30, min.position.ic = 0,
  normalise.scores = c(FALSE, TRUE), min.overlap = 6, min.mean.ic = 0.25,
  progress = TRUE, nthreads = 1, tryRC = TRUE, score.strat = c("sum",
  "a.mean", "g.mean", "median", "wa.mean", "wg.mean", "fzt"))
make_DBscores(db.motifs, method = c("PCC", "EUCL", "SW", "KL", "WEUCL",
  "ALLR", "BHAT", "HELL", "WPCC", "SEUCL", "MAN", "ALLR_LL"),
  shuffle.db = TRUE, shuffle.k = 3, shuffle.method = "linear",
  rand.tries = 1000, widths = 5:30, min.position.ic = 0,
  normalise.scores = c(FALSE, TRUE), min.overlap = 6, min.mean.ic = 0.25,
  progress = TRUE, nthreads = 1, tryRC = TRUE, score.strat = c("sum",
  "a.mean", "g.mean", "median", "wa.mean", "wg.mean", "fzt"))

Arguments

`db.motifs`	`list` Database motifs.
`method`	`character(1)` One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`shuffle.db`	`logical(1)` Deprecated. Does nothing. generate random motifs with `create_motif()`.
`shuffle.k`	`numeric(1)` See `shuffle_motifs()`.
`shuffle.method`	`character(1)` See `shuffle_motifs()`.
`rand.tries`	`numeric(1)` Approximate number of comparisons to perform for every combination of `widths`.
`widths`	`numeric` Motif widths to use in P-value database calculation.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`progress`	`logical(1)` Show progress.
`nthreads`	`numeric(1)` Run `compare_motifs()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.

Details

See compare_motifs() for more info on comparison parameters.

To replicate the internal universalmotif DB scores, run make_DBscores() with the default settings. Note that this will be a slow process.

Arguments widths, method, normalise.scores and score.strat are vectorized; all combinations will be attempted.

Value

A DataFrame with score distributions for the input database. If more than one make_DBscores() run occurs (i.e. args method, normalise.scores or score.strat are longer than 1), then the function args are included in the metadata slot.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Examples

## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb[1:100])
scores <- make_DBscores(motifs, method = "PCC")
compare_motifs(motifs, 1:100, db.scores = scores)

## End(Not run)

## Not run: 
library(MotifDb)
motifs <- convert_motifs(MotifDb[1:100])
scores <- make_DBscores(motifs, method = "PCC")
compare_motifs(motifs, 1:100, db.scores = scores)

## End(Not run)

Merge motifs.

Description

Aligns the motifs using compare_motifs(), then averages the motif PPMs. Currently the multifreq slot, if filled in any of the motifs, will be dropped. Only 0-order background probabilities will be kept. Motifs are merged one at a time, starting with the first entry in the list.

Usage

merge_motifs(motifs, method = "ALLR", use.type = "PPM", min.overlap = 6,
  min.mean.ic = 0.25, tryRC = TRUE, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  new.name = NULL)
merge_motifs(motifs, method = "ALLR", use.type = "PPM", min.overlap = 6,
  min.mean.ic = 0.25, tryRC = TRUE, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  new.name = NULL)

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`method`	`character(1)` One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`use.type`	`character(1)` One of `'PPM'` and `'ICM'`. The latter allows for taking into account the background frequencies if `relative_entropy = TRUE`. Note that `'ICM'` is not allowed when `method = c("ALLR", "ALLR_LL")`.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
`new.name`	`character(1)`, `NULL` Instead of collapsing existing names (if `NULL`), assign a new one manually for the merged motif.

Details

See compare_motifs() for more info on comparison parameters.

If using a comparison metric where 0s are not allowed (KL, ALLR, ALLR_LL, IS), then pseudocounts will be added internally. These pseudocounts are only used for comparison and alignment, and are not used in the final merging step.

Note: score.strat = "a.mean" is NOT recommended, as merge_motifs() will not discriminate between two alignments with equal mean scores, even if one alignment is longer than the other.

Value

A single motif object. See convert_motifs() for available formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Not run: 
library(MotifDb)
merged.motif <- merge_motifs(MotifDb[1:5])

## End(Not run)

m1 <- create_motif("TTAAACCCC", name = "1")
m2 <- create_motif("AACC", name = "2")
m3 <- create_motif("AACCCCGG", name = "3")
view_motifs(merge_motifs(c(m1, m2, m3)))

## Not run: 
library(MotifDb)
merged.motif <- merge_motifs(MotifDb[1:5])

## End(Not run)

m1 <- create_motif("TTAAACCCC", name = "1")
m2 <- create_motif("AACC", name = "2")
m3 <- create_motif("AACCCCGG", name = "3")
view_motifs(merge_motifs(c(m1, m2, m3)))

Identify and merge similar motifs within a collection of motifs (or simply cluster motifs).

Description

Given a list of motifs, merge_similar() will identify similar motifs with compare_motifs(), and merge similar ones with merge_motifs().

Usage

merge_similar(motifs, threshold = 0.95, threshold.type = "score.abs",
  method = "PCC", use.type = "PPM", min.overlap = 6, min.mean.ic = 0,
  tryRC = TRUE, relative_entropy = FALSE, normalise.scores = FALSE,
  min.position.ic = 0, score.strat.compare = "a.mean",
  score.strat.merge = "sum", nthreads = 1, return.clusters = FALSE)
merge_similar(motifs, threshold = 0.95, threshold.type = "score.abs",
  method = "PCC", use.type = "PPM", min.overlap = 6, min.mean.ic = 0,
  tryRC = TRUE, relative_entropy = FALSE, normalise.scores = FALSE,
  min.position.ic = 0, score.strat.compare = "a.mean",
  score.strat.merge = "sum", nthreads = 1, return.clusters = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`threshold`	`numeric(1)` The minimum (for similarity metrics) or maximum (for distance metrics) threshold score for merging.
`threshold.type`	`character(1)` Type of score used for thresholding. Currently unused.
`method`	`character(1)` One of PCC, EUCL, SW, KL, BHAT, HELL, SEUCL, MAN, WEUCL, WPCC. See `compare_motifs()`. (The ALLR and ALLR_LL methods cannot be used for distance matrix construction.)
`use.type`	`character(1)` One of `'PPM'` and `'ICM'`. The latter allows for taking into account the background frequencies if `relative_entropy = TRUE`. Note that `'ICM'` is not allowed when `method = c("ALLR", "ALLR_LL")`.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`score.strat.compare`	`character(1)` The `score.strat` parameter used by `compare_motifs()`. For clustering purposes, the `"sum"` option cannot be used.
`score.strat.merge`	`character(1)` The `score.strat` parameter used by `merge_motifs()`. As discussed in `merge_motifs()`, the `"sum"` option is recommended over `"a.mean"` to maximize the overlap between motifs.
`nthreads`	`numeric(1)` Run `compare_motifs()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads.
`return.clusters`	`logical(1)` Return the clusters instead of merging.

Details

See compare_motifs() for more info on comparison parameters, and merge_motifs() for more info on motif merging.

Value

See convert_motifs() for available output formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Not run: 
library(MotifDb)
motifs <- filter_motifs(MotifDb, family = "bHLH")[1:50]
length(motifs)
motifs <- merge_similar(motifs)
length(motifs)

## End(Not run)

## Not run: 
library(MotifDb)
motifs <- filter_motifs(MotifDb, family = "bHLH")[1:50]
length(motifs)
motifs <- merge_similar(motifs)
length(motifs)

## End(Not run)

Look for overrepresented motif position peaks in a set of sequences.

Description

Using the motif position data from scan_sequences() (or elsewhere), test whether certain positions in the sequences have significantly higher motif density.

Usage

motif_peaks(hits, seq.length, seq.count, bandwidth, max.p = 1e-06,
  peak.width = 3, nrand = 100, plot = TRUE, BP = FALSE)
motif_peaks(hits, seq.length, seq.count, bandwidth, max.p = 1e-06,
  peak.width = 3, nrand = 100, plot = TRUE, BP = FALSE)

Arguments

`hits`	`numeric` A vector of sequence positions indicating motif sites.
`seq.length`	`numeric(1)` Length of sequences. Only one number is allowed, as all sequences must be of identical length. If missing, then the largest number from `hits` is used.
`seq.count`	`numeric(1)` Number of sequences with motif sites. If missing, then the number of unique values in `hits` is used.
`bandwidth`	`numeric(1)` Peak smoothing parameter. Smaller numbers will result in skinnier peaks, larger numbers will result in wider peaks. Leaving this empty will cause `motif_peaks()` to generate one by itself (see 'details').
`max.p`	`numeric(1)` Maximum P-value allowed for finding significant motif site peaks.
`peak.width`	`numeric(1)` Minimum peak width. A peak is defined as as the highest point within the value set by `peak.width`.
`nrand`	`numeric(1)` Number of random permutations for generating a null distribution. In order to calculate P-values, a set of random motif site positions are generated `nrand` times.
`plot`	`logical(1)` Will create a `ggplot2` object displaying motif peaks.
`BP`	`logical(1)` Allows for the use of BiocParallel within `motif_peaks()`. See `BiocParallel::register()` to change the default backend. Setting `BP = TRUE` is only recommended for exceptionally large jobs. Keep in mind that this function will not attempt to limit its memory usage.

Details

Kernel smoothing is used to calculate motif position density. The implementation for this process is based on code from the KernSmooth R package (Wand 2015). These density estimates are used to determine peak locations and heights. To calculate the P-values of these peaks, a null distribution is calculated from peak heights of randomly generated motif positions.

If the bandwidth option is not supplied, then the following code is used (from KernSmooth):

del0 <- (1 / (4 * pi))^(1 / 10)

bandwidth <- del0 * (243 / (35 * length(hits)))^(1 / 5) * sqrt(var(hits))

Value

A DataFrame with peak positions and P-values. If plot = TRUE, then a list is returned with the DataFrame as the first item and the ggplot2 object as the second item.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Wand M (2015). KernSmooth: Functions for Kernel Smoothing Supporting Wand and Jones (1995). R package version 2.23-15, <URL: https://CRAN.R-project.org/package=KernSmooth>.

Examples

data(ArabidopsisMotif)
data(ArabidopsisPromoters)
if (R.Version()$arch != "i386") {
hits <- scan_sequences(ArabidopsisMotif, ArabidopsisPromoters, RC = FALSE)
res <- motif_peaks(as.vector(hits$start), 1000, 50)
# View plot:
res$Plot

# The raw plot data can be found in:
res$Plot$data
}

data(ArabidopsisMotif)
data(ArabidopsisPromoters)
if (R.Version()$arch != "i386") {
hits <- scan_sequences(ArabidopsisMotif, ArabidopsisPromoters, RC = FALSE)
res <- motif_peaks(as.vector(hits$start), 1000, 50)
# View plot:
res$Plot

# The raw plot data can be found in:
res$Plot$data
}

Motif P-value and scoring utility

Description

For calculating P-values and logodds scores from P-values for any number of motifs.

Usage

motif_pvalue(motifs, score, pvalue, bkg.probs, use.freq = 1, k = 8,
  nthreads = 1, rand.tries = 10, rng.seed = sample.int(10000, 1),
  allow.nonfinite = FALSE, method = c("dynamic", "exhaustive"))
motif_pvalue(motifs, score, pvalue, bkg.probs, use.freq = 1, k = 8,
  nthreads = 1, rand.tries = 10, rng.seed = sample.int(10000, 1),
  allow.nonfinite = FALSE, method = c("dynamic", "exhaustive"))

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`score`	`numeric`, `list` Get a P-value for a motif from a logodds score. See details for an explanation of how to vectorize the calculation for `method = "dynamic"`.
`pvalue`	`numeric`, `list` Get a logodds score for a motif from a P-value. See details for an explanation of how to vectorize the calculation for `method = "dynamic"`.
`bkg.probs`	`numeric`, `list` A vector background probabilities. If supplying individual background probabilities for each motif, a list of such vectors. If missing, retrieves the background from the motif `bkg` slot. Note that this option is only used when `method = "dynamic"`, or when `method = "exhaustive"` and providing a P-value and returning a score; for the inverse, the motifs are first converted to PWMs via `convert_type()`, which uses the motif `bkg` slot for background adjustment.
`use.freq`	`numeric(1)` By default uses the regular motif matrix; otherwise uses the corresponding `multifreq` matrix. Max is 3 when `method = "exhaustive"`.
`k`	`numeric(1)` For speed, scores/P-values can be approximated after subsetting the motif every `k` columns when `method = "exhaustive"`. If `k` is a value equal or higher to the size of input motif(s), then the calculations are exact. The default, 8, is recommended to those looking for a good tradeoff between speed and accuracy for jobs requiring repeated calculations. Note that this is ignored when `method = "dynamic"`, as subsetting is not required.
`nthreads`	`numeric(1)` Run `motif_pvalue()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Currently only applied when `method = "exhaustive"`.
`rand.tries`	`numeric(1)` When `ncol(motif) < k` and `method = "exhaustive"`, an approximation is used. This involves randomly approximating the overall motif score distribution. To increase accuracy, the distribution is approximated `rand.tries` times and the final scores averaged. Note that this is ignored when `method = "dynamic"`, as subsetting is not required.
`rng.seed`	`numeric(1)` In order to allow `motif_pvalue()` to perform C++ level parallelisation, it must work independently from R. This means it cannot communicate with R to get/set the R RNG state. To get around this, the RNG seed used by the C++ function can be set with `rng.seed`. To make sure each thread gets a different seed however, the seed is multiplied with the iteration count. For example: when working with two motifs, the second motif gets the following seed: `rng.seed * 2`. The default is to pick a random number as chosen by `sample()`, which effectively makes `motif_pvalue()` dependent on the R RNG state. Note that this is ignored when `method = "dynamic"`, as the random subsetting is only used for `method = "exhaustive"`.
`allow.nonfinite`	`logical(1)` If `FALSE`, then apply a pseudocount if non-finite values are found in the PWM. Note that if the motif has a pseudocount greater than zero and the motif is not currently of type PWM, then this parameter has no effect as the pseudocount will be applied automatically when the motif is converted to a PWM internally. Note that this option is incompatible with `method = "dynamic"`. A message will be printed if a pseudocount is applied. To disable this, set `options(pseudocount.warning=FALSE)`.
`method`	`character(1)` One of `c("dynamic", "exhaustive")`. Algorithm used for calculating P-values. The `"exhaustive"` method involves finding all possible motif matches at or above the specified score using a branch-and-bound algorithm, which can be computationally intensive (Hartman et al., 2013). Additionally, the computation must be repeated for each hit. The `"dynamic"` method calculates the distribution of possible motif scores using a much faster dynamic programming algorithm, and can be recycled for multiple scores (Grant et al., 2011). The only disadvantage is the inability to use `allow.nonfinite = TRUE`.

Details

Regarding vectorization

A note regarding vectorizing the calculation when method = "dynamic" (no vectorization is possible with method = "exhaustive"): to avoid performing the P-value/score calculation repeatedly for individual motifs, provide the score/pvalue arguments as a list, with each entry corresponding to the scores/P-values to be calculated for the respective motifs provided to motifs. If you simply provide a list of repeating motifs and a single numeric vector of corresponding input scores/P-values, then motif_pvalue() will not vectorize. See the Examples section.

The dynamic method

One of the algorithms available to motif_pvalue() to calculate scores or P-values is the dynamic programming algorithm used by FIMO (Grant et al., 2011). In this method, a small range of possible scores from the possible miminum and maximum is created and the cumulative probability of each score in this distribution is incrementally calculated using the logodds scores and the background probabilities. This distribution of scores and associated P-values can be used to calculate P-values or scores for any input, any number of times. This method scales well with large motifs, and multifreq representations. The only downside is that it is incompatible with allow.nonfinite = TRUE, as this would not allow for the creation of the initial range of scores. Although described for a different purpose, the basic premise of the dynamic programming algorithm is also described in Gupta et al. (2007).

The exhaustive method

Calculating P-values exhaustively for motifs can be very computationally intensive. This is due to how P-values must be calculated: for a given score, all possible sequences which score equal or higher must be found, and the probability for each of these sequences (based on background probabilities) summed. For a DNA motif of length 10, the number of possible unique sequences is 4^10 = 1,048,576. Finding all possible sequences higher than a given score can be done very efficiently and quickly with a branch-and-bound algorithm, but as the motif length increases even this calculation becomes impractical. To get around this, the P-value calculation can be approximated.

In order to calculate P-values for longer motifs, this function uses the approximation proposed by Hartmann et al. (2013), where the motif is subset, P-values calculated for the subsets, and finally combined for a total P-value. The smaller the size of the subsets, the faster the calculation; but also, the bigger the approximation. This can be controlled by setting k. In fact, for smaller motifs (< 13 positions) calculating exact P-values can be done individually in reasonable time by setting k = 12.

To calculate a score from a P-value, all possible scores are calculated and the (1 - pvalue) * 100 nth percentile score returned. When k < ncol(motif), the complete set of scores is instead approximated by randomly adding up all possible scores from each subset. Note that this approximation can actually be potentially quite expensive at times and even slower than the exact version; for jobs requiring lots of repeat calculations, a bit of benchmarking beforehand can be useful to find the optimal settings.

Please note that bugs are more likely to occur when using the exhaustive method, as the algorithm contains several times more code compared to the dynamic method. Unless you have a strong need to use allow.nonfinite = TRUE then avoid using this method.

Value

numeric, list A vector or list of vectors of scores/P-values.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Grant CE, Bailey TL, Noble WS (2011). "FIMO: scanning for occurrences of a given motif." Bioinformatics, 27, 1017-1018.

Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007). "Quantifying similarity between motifs." Genome Biology, 8, R24.

Hartmann H, Guthohrlein EW, Siebert M, Soding SLJ (2013). “P-value-based regulatory motif discovery using positional weight matrices.” Genome Research, 23, 181-194.

Examples

if (R.Version()$arch != "i386") {

## P-value/score calculations are performed using the PWM version of the
## motif
data(examplemotif)

## Get a minimum score based on a P-value
motif_pvalue(examplemotif, pvalue = 0.001)

## Get the probability of a particular sequence hit
motif_pvalue(examplemotif, score = 0)

## The calculations can be performed for multiple motifs
motif_pvalue(c(examplemotif, examplemotif), pvalue = c(0.001, 0.0001))

## Compare score thresholds and P-value:
scores <- motif_score(examplemotif, c(0.6, 0.7, 0.8, 0.9))
motif_pvalue(examplemotif, scores)

## Calculate the probability of getting a certain match or better:
TATATAT <- score_match(examplemotif, "TATATAT")
TATATAG <- score_match(examplemotif, "TATATAG")
motif_pvalue(examplemotif, TATATAT)
motif_pvalue(examplemotif, TATATAG)

## Get all possible matches by P-value:
get_matches(examplemotif, motif_pvalue(examplemotif, pvalue = 0.0001))

## Vectorize the calculation for multiple motifs and scores/P-values:
m <- create_motif()
motif_pvalue(c(examplemotif, m), list(1:5, 2:3))
## The non-vectorized equivalent:
motif_pvalue(
  c(rep(list(examplemotif), 5), rep(list(m), 2)), c(1:5, 2:3)
)
}

if (R.Version()$arch != "i386") {

## P-value/score calculations are performed using the PWM version of the
## motif
data(examplemotif)

## Get a minimum score based on a P-value
motif_pvalue(examplemotif, pvalue = 0.001)

## Get the probability of a particular sequence hit
motif_pvalue(examplemotif, score = 0)

## The calculations can be performed for multiple motifs
motif_pvalue(c(examplemotif, examplemotif), pvalue = c(0.001, 0.0001))

## Compare score thresholds and P-value:
scores <- motif_score(examplemotif, c(0.6, 0.7, 0.8, 0.9))
motif_pvalue(examplemotif, scores)

## Calculate the probability of getting a certain match or better:
TATATAT <- score_match(examplemotif, "TATATAT")
TATATAG <- score_match(examplemotif, "TATATAG")
motif_pvalue(examplemotif, TATATAT)
motif_pvalue(examplemotif, TATATAG)

## Get all possible matches by P-value:
get_matches(examplemotif, motif_pvalue(examplemotif, pvalue = 0.0001))

## Vectorize the calculation for multiple motifs and scores/P-values:
m <- create_motif()
motif_pvalue(c(examplemotif, m), list(1:5, 2:3))
## The non-vectorized equivalent:
motif_pvalue(
  c(rep(list(examplemotif), 5), rep(list(m), 2)), c(1:5, 2:3)
)
}

Get the reverse complement of a DNA or RNA motif.

Description

For any motif, change the motif slot to it's reverse complement. If the multifreq slot is filled, then it is also applied. No other slots are affected.

Usage

motif_rc(motifs, ignore.alphabet = FALSE)
motif_rc(motifs, ignore.alphabet = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats
`ignore.alphabet`	`logical(1)` If `TRUE`, then `motif_rc()` throws an error when it detects a non-DNA/RNA motif. If `FALSE`, it will proceed regardless.

Value

See convert_motifs() for available output formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.rc <- motif_rc(jaspar)

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.rc <- motif_rc(jaspar)

Generate ggplot2 motif trees with ggtree.

Description

For more powerful motif tree functions, see the motifStack package. The motif_tree() function compares motifs with compare_motifs() to create a distance matrix, which is used to generate a phylogeny. This can be plotted with ggtree::ggtree(). The purpose of this function is simply to combine the compare_motifs() and ggtree::ggtree() steps into one. For more control over tree creation, it is recommend to do these steps separately. See the "Motif comparisons and P-values" vignette for such a workthrough. This function requires the ape and ggtree packages to be installed separately.

Usage

motif_tree(motifs, layout = "circular", linecol = "family",
  labels = "none", tipsize = "none", legend = TRUE,
  branch.length = "none", db.scores, method = "EUCL", use.type = "PPM",
  min.overlap = 6, min.position.ic = 0, tryRC = TRUE, min.mean.ic = 0,
  relative_entropy = FALSE, progress = FALSE, nthreads = 1,
  score.strat = "a.mean", ...)
motif_tree(motifs, layout = "circular", linecol = "family",
  labels = "none", tipsize = "none", legend = TRUE,
  branch.length = "none", db.scores, method = "EUCL", use.type = "PPM",
  min.overlap = 6, min.position.ic = 0, tryRC = TRUE, min.mean.ic = 0,
  relative_entropy = FALSE, progress = FALSE, nthreads = 1,
  score.strat = "a.mean", ...)

Arguments

`motifs`	`list`, `dist` See `convert_motifs()` for available formats. Alternatively, the resulting comparison matrix from `compare_motifs()` (run `as.dist(results)` beforehand; if the comparison was performed with a similarity metric, make sure to convert to distances first).
`layout`	`character(1)` One of `c('rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle', 'daylight')`. See `ggtree::ggtree()`.
`linecol`	`character(1)` universalmotif slot to use to colour lines (e.g. 'family'). Not available for `dist` input (see examples for how to add it manually). See `ggtree::ggtree()`.
`labels`	`character(1)` universalmotif slot to use to label tips (e.g. 'name'). For `dist` input, only 'name' is available. See `ggtree::ggtree()`.
`tipsize`	`character(1)` universalmotif slot to use to control tip size (e.g. 'icscore'). Not available for `dist` input (see examples for how to add it manually). See `ggtree::ggtree()`.
`legend`	`logical(1)` Show legend for line colour and tip size. See `ggtree::ggtree()`.
`branch.length`	`character(1)` If 'none', draw a cladogram. See `ggtree::ggtree()`.
`db.scores`	`data.frame` See `compare_motifs()`.
`method`	`character(1)` One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`use.type`	`character(1)`c('PPM', 'ICM')`⁠. The latter allows for taking into account the background frequencies (only if ⁠`relative_entropy = TRUE'). See `compare_motifs()`.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`progress`	`logical(1)` Show message regarding current step.
`nthreads`	`numeric(1)` Run `compare_motifs()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
`...`	ggtree params. See `ggtree::ggtree()`.

Details

See compare_motifs() for more info on comparison parameters.

Value

ggplot object.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Wickham H (2009). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-0-387-98140-6, <URL: http://ggplot2.org>.

Yu G, Smith D, Zhu H, Guan Y, Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, 28-36. doi: 10.1111/2041-210X.12628.

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
if (requireNamespace("ggtree", quietly = TRUE)) {
jaspar.tree <- motif_tree(jaspar, linecol = "none", labels = "name",
                          layout = "rectangular")
}

## Not run: 
## When inputting a dist object, the linecol and tipsize options are
## not available. To add these manually:

library(MotifDb)
library(ggtree)
library(ggplot2)

motifs <- filter_motifs(MotifDb, organism = "Athaliana")[1:50]
comparison <- compare_motifs(motifs, method = "PCC", score.strat = "a.mean")
comparison <- as.dist(1 - comparison)
mot.names <- attr(comparison, "Labels")
tree <- motif_tree(comparison)

annotations <- data.frame(label = mot.names,
                          icscore = sapply(motifs, function(x) x["icscore"]),
                          family = sapply(motifs, function(x) x["family"]))

tree <- tree %<+% annotations +
          geom_tippoint(aes(size = icscore)) +
          aes(colour = family) +
          theme(legend.position = "right",
                legend.title = element_blank())

## End(Not run)

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
if (requireNamespace("ggtree", quietly = TRUE)) {
jaspar.tree <- motif_tree(jaspar, linecol = "none", labels = "name",
                          layout = "rectangular")
}

## Not run: 
## When inputting a dist object, the linecol and tipsize options are
## not available. To add these manually:

library(MotifDb)
library(ggtree)
library(ggplot2)

motifs <- filter_motifs(MotifDb, organism = "Athaliana")[1:50]
comparison <- compare_motifs(motifs, method = "PCC", score.strat = "a.mean")
comparison <- as.dist(1 - comparison)
mot.names <- attr(comparison, "Labels")
tree <- motif_tree(comparison)

annotations <- data.frame(label = mot.names,
                          icscore = sapply(motifs, function(x) x["icscore"]),
                          family = sapply(motifs, function(x) x["family"]))

tree <- tree %<+% annotations +
          geom_tippoint(aes(size = icscore)) +
          aes(colour = family) +
          theme(legend.position = "right",
                legend.title = element_blank())

## End(Not run)

Import CIS-BP motifs.

Description

Import CIS-BP formatted motifs. See http://cisbp.ccbr.utoronto.ca/index.php. Assumed to be DNA motifs.

Usage

read_cisbp(file, skip = 0)
read_cisbp(file, skip = 0)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.

Details

CIS-BP motifs can be formatted with or without additional header metadata. Motifs without any header start at instances of the word "Pos", whereas motifs with a header start at instances of the word "TF".

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR (2014). “Determination and inference of eukaryotic transcription factor sequence specificity.” Cell, 158, 1431-1443.

Examples

cisbp <- read_cisbp(system.file("extdata", "cisbp.txt",
                                package = "universalmotif"))

cisbp <- read_cisbp(system.file("extdata", "cisbp.txt",
                                package = "universalmotif"))

Import HOMER motifs.

Description

Import HOMER formatted motifs. See http://homer.ucsd.edu/homer/motif/. Assumed to be DNA motifs. Note that HOMER motifs come with a pre-determined logodds threshold; if you wish to re-create HOMER's motif scanning, then use it in scan_sequences() (see examples).

Usage

read_homer(file, skip = 0)
read_homer(file, skip = 0)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010). “Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.” Molecular Cell, 38, 576-589.

Examples

data(ArabidopsisPromoters)
homer <- read_homer(system.file("extdata", "homer.txt",
                                package = "universalmotif"))
thresholds <- homer |> to_df() |> with(logodds.threshold) |> as.numeric()
scan_sequences(homer, ArabidopsisPromoters,
  threshold = thresholds, threshold.type = "logodds.abs")

data(ArabidopsisPromoters)
homer <- read_homer(system.file("extdata", "homer.txt",
                                package = "universalmotif"))
thresholds <- homer |> to_df() |> with(logodds.threshold) |> as.numeric()
scan_sequences(homer, ArabidopsisPromoters,
  threshold = thresholds, threshold.type = "logodds.abs")

Import JASPAR motifs.

Description

Import JASPAR formatted motifs. See http://jaspar.genereg.net/. Can be either DNA, RNA, or AA motifs.

Usage

read_jaspar(file, skip = 0)
read_jaspar(file, skip = 0)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))

Import motifs from raw matrices.

Description

Import simply formatted motifs.

Usage

read_matrix(file, skip = 0, type, positions = "columns",
  alphabet = "DNA", sep = "", headers = TRUE, rownames = FALSE,
  comment = NULL)
read_matrix(file, skip = 0, type, positions = "columns",
  alphabet = "DNA", sep = "", headers = TRUE, rownames = FALSE,
  comment = NULL)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`. If missing will try and guess which one.
`positions`	`character(1)` One of `c('columns', 'rows')`. Partial matching allowed. Indicate whether each position within a motif is represented as a row or a column in the file.
`alphabet`	`character(1)` One of `c('DNA', 'RNA', 'AA')`, or a string of letters.
`sep`	`character(1)` Indicates how individual motifs are separated. Set as `NULL` if there are no seperating lines between motifs (the default is to assume a blank line).
`headers`	`logical(1)`, `character(1)` Indicating if and how to read names.
`rownames`	`logical(1)` Are there alphabet letters present as rownames?
`comment`	`NULL`, `character(1)` Character denoting lines to be considered comments.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

   hocomoco <- system.file("extdata", "hocomoco.txt", package = "universalmotif")
   hocomoco <- read_matrix(hocomoco, headers = ">", positions = "rows")

hocomoco <- system.file("extdata", "hocomoco.txt", package = "universalmotif")
   hocomoco <- read_matrix(hocomoco, headers = ">", positions = "rows")

Import MEME motifs.

Description

Import MEME formatted motifs, as well as original motif sequences. See http://meme-suite.org/doc/meme-format.html. Both 'full' and 'minimal' formats are supported. DREME and STREME motifs can also be imported, but note that readsites and readsites.meta arguments do nothing.

Usage

read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE,
  readsites.meta.tidy = FALSE)
read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE,
  readsites.meta.tidy = FALSE)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.
`readsites`	`logical(1)` If `TRUE`, the motif sites will be read as well.
`readsites.meta`	`logical(1)` If `readsites = TRUE`, then additionally read site positions and P-values.
`readsites.meta.tidy`	`logical(1)` If `readsites.meta = TRUE`, merge the position site information for all motifs into a single tidy `data.frame`.

Details

Please note that the typical number precision limit in R is around 1e-308. This means that motif P-values in MEME files below this limit are rounded automatically to 0. To get around this, the E-value is also stored as a string in the extrainfo slot. If you require a numeric value for analysis, use the log_string_pval() function to get the log of the string-formatted p-value.

Value

list universalmotif objects. If readsites = TRUE, a list comprising of a sub-list of motif objects and a sub-list of motif sites will be returned. If readsites.meta = TRUE, then two additional list items will be present, one containing site positions and P-values, and another containing combined sequence p-values. If readsites.meta.tidy = TRUE, an additional list entry named sites.meta.tidy will be added containing a data.frame.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009). “MEME SUITE: tools for motif discovery and searching.” Nucleic Acids Research, 37, W202-W208.

Examples

meme.minimal <- read_meme(system.file("extdata", "meme_minimal.txt",
                                      package = "universalmotif"))
meme.full <- read_meme(system.file("extdata", "meme_full.txt",
                                   package = "universalmotif"))
## Get numeric p-value:
log_string_pval(meme.minimal[[1]]["extrainfo"]["eval.string"])

meme.minimal <- read_meme(system.file("extdata", "meme_minimal.txt",
                                      package = "universalmotif"))
meme.full <- read_meme(system.file("extdata", "meme_full.txt",
                                   package = "universalmotif"))
## Get numeric p-value:
log_string_pval(meme.minimal[[1]]["extrainfo"]["eval.string"])

Import universalmotif formatted motifs.

Description

Import motifs created from write_motifs(). For optimal storage of universalmotif class motifs, consider using saveRDS() and readRDS(). Currently the universalmotif format is YAML-based, but this is subject to change.

Usage

read_motifs(file, skip = 0, progress = FALSE, BP = FALSE)
read_motifs(file, skip = 0, progress = FALSE, BP = FALSE)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.
`progress`	`logical(1)` Show progress.
`BP`	`logical(1)` Allows for the use of BiocParallel within `read_motifs()`. See `BiocParallel::register()` to change the default backend.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Import TRANSFAC motifs.

Description

Import TRANSFAC formatted motifs. Assumed to be DNA motifs, type PCM. See system.file("extdata", "transfac.txt", pacakge="universalmotif") for an example motif.

Usage

read_transfac(file, skip = 0)
read_transfac(file, skip = 0)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.

Details

A few TRANSFAC tags are recognized, including AC, ID, NA, HC and OS. HC will be set to the family slot and OS to the organism slot. If AC, ID and NA are present, then AC will be set as the motif name and NA as the alternate name. If AC is absent, then ID is set as the name. If ID is also absent, then NA is set as the motif name.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Wingender E, Dietze P, Karas H, Knuppel R (1996). “TRANSFAC: A Database on Transcription Factors and Their DNA Binding Sites.” Nucleic Acids Research, 24, 238-241.

Examples

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                      package = "universalmotif"))

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                      package = "universalmotif"))

Import UNIPROBE motifs.

Description

Import UNIPROBE formatted motifs. Assumed DNA.

Usage

read_uniprobe(file, skip = 0)
read_uniprobe(file, skip = 0)

Arguments

`file`	`character(1)` File name.
`skip`	`numeric(1)` If not zero, will skip however many desired lines in the file before starting to read.

Value

list universalmotif objects.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML (2015). “UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.” Nucleic Acids Research, 43, D117-D122.

Examples

uniprobe.minimal <- read_uniprobe(system.file("extdata", "uniprobe_minimal.txt",
                                              package = "universalmotif"))
uniprobe.full <- read_uniprobe(system.file("extdata", "uniprobe_full.txt",
                                           package = "universalmotif"))

uniprobe.minimal <- read_uniprobe(system.file("extdata", "uniprobe_minimal.txt",
                                              package = "universalmotif"))
uniprobe.full <- read_uniprobe(system.file("extdata", "uniprobe_full.txt",
                                           package = "universalmotif"))

Run MEME from within R.

Description

De novo motif discovery via MEME. For a detailed description of the command, see http://meme-suite.org/doc/meme.html. For a brief description of the command parameters, call run_meme() without any arguments. Parameters in run_meme() which are directly taken from the MEME program are tagged with [MEME]. This function requires that the processx package be installed separately.

Usage

run_meme(target.sequences, output = NULL, overwrite.dir = FALSE,
  control.sequences = NULL, weights = NULL, text = FALSE, brief = 1000,
  objfun = "classic", test = NULL, use_llr = FALSE, shuf = 2,
  hsfrac = NULL, cefrac = NULL, searchsize = NULL, norand = FALSE,
  csites = 1000, seed = 0, alph = NULL, revcomp = FALSE, pal = FALSE,
  mod = "zoops", nmotifs = 3, evt = NULL, nsites = NULL,
  minsites = NULL, maxsites = NULL, wnsites = 0.8, w = NULL,
  minw = 8, maxw = 50, allw = NULL, nomatrim = FALSE, wg = 11,
  ws = 1, noendgaps = FALSE, bfile = NULL, markov_order = 0,
  psp = NULL, maxiter = 50, distance = 0.001, prior = NULL, b = NULL,
  plib = NULL, spfuzz = NULL, spmap = NULL, cons = NULL, p = NULL,
  maxsize = NULL, maxtime = NULL, wd = getwd(), logfile = paste0(wd,
  "/memerun.log"), readsites = TRUE, echo = FALSE, verbose = 1,
  timeout = Inf, bin = getOption("meme.bin"))
run_meme(target.sequences, output = NULL, overwrite.dir = FALSE,
  control.sequences = NULL, weights = NULL, text = FALSE, brief = 1000,
  objfun = "classic", test = NULL, use_llr = FALSE, shuf = 2,
  hsfrac = NULL, cefrac = NULL, searchsize = NULL, norand = FALSE,
  csites = 1000, seed = 0, alph = NULL, revcomp = FALSE, pal = FALSE,
  mod = "zoops", nmotifs = 3, evt = NULL, nsites = NULL,
  minsites = NULL, maxsites = NULL, wnsites = 0.8, w = NULL,
  minw = 8, maxw = 50, allw = NULL, nomatrim = FALSE, wg = 11,
  ws = 1, noendgaps = FALSE, bfile = NULL, markov_order = 0,
  psp = NULL, maxiter = 50, distance = 0.001, prior = NULL, b = NULL,
  plib = NULL, spfuzz = NULL, spmap = NULL, cons = NULL, p = NULL,
  maxsize = NULL, maxtime = NULL, wd = getwd(), logfile = paste0(wd,
  "/memerun.log"), readsites = TRUE, echo = FALSE, verbose = 1,
  timeout = Inf, bin = getOption("meme.bin"))

Arguments

`target.sequences`	`XStringSet` List of sequences to get motifs from.
`output`	`character(1)` Name of the output folder. If `NULL`, MEME output will be deleted.
`overwrite.dir`	`logical(1)` If `output` is set but already exists, allow over-writing.
`control.sequences`	`XStringSet` List of negative sequences. Only used if `objfun = c("de", "se")`.
`weights`	`numeric` Vector of numbers between 0 and 1, representing sequence weights.
`text`	`logical(1)` [MEME]
`brief`	`numeric(1)` [MEME]
`objfun`	`character(1)` [MEME]
`test`	`character(1)` [MEME]
`use_llr`	`logical(1)` [MEME]
`shuf`	`numeric(1)` [MEME]
`hsfrac`	`numeric(1)` [MEME]
`cefrac`	`numeric(1)` [MEME]
`searchsize`	`numeric(1)` [MEME]
`norand`	`logical(1)` [MEME]
`csites`	`numeric(1)` [MEME]
`seed`	`numeric(1)` [MEME]
`alph`	`character(1)` [MEME] Note: custom alphabet definition files can be created using `meme_alph()`.
`revcomp`	`logical(1)` [MEME]
`pal`	`logical(1)` [MEME]
`mod`	`character(1)` [MEME]
`nmotifs`	`numeric(1)` [MEME]
`evt`	`numeric(1)` [MEME]
`nsites`	`numeric(1)` [MEME]
`minsites`	`numeric(1)` [MEME]
`maxsites`	`numeric(1)` [MEME]
`wnsites`	`numeric(1)` [MEME]
`w`	`numeric(1)` [MEME]
`minw`	`numeric(1)` [MEME]
`maxw`	`numeric(1)` [MEME]
`allw`	`numeric(1)` [MEME]
`nomatrim`	`logical(1)` [MEME]
`wg`	`numeric(1)` [MEME]
`ws`	`numeric(1)` [MEME]
`noendgaps`	`logical(1)` [MEME]
`bfile`	`character(1)` [MEME]
`markov_order`	`numeric(1)` [MEME]
`psp`	`character(1)` [MEME]
`maxiter`	`numeric(1)` [MEME]
`distance`	`numeric(1)` [MEME]
`prior`	`character(1)` [MEME]
`b`	`numeric(1)` [MEME]
`plib`	`character(1)` [MEME]
`spfuzz`	`numeric(1)` [MEME]
`spmap`	`character(1)` [MEME]
`cons`	`character(1)` [MEME]
`p`	`numeric(1)` [MEME]
`maxsize`	`numeric(1)` [MEME]
`maxtime`	`numeric(1)` [MEME]
`wd`	`character(1)` Working directory to run MEME in.
`logfile`	`character(1)` File to dump MEME stderr. If `NULL`, no logs will be saved.
`readsites`	`logical(1)` Read sites from MEME output (from `read_meme()`).
`echo`	`logical(1)` Dump MEME output to console.
`verbose`	`numeric(1)` Set `verbose = 0` to quiet `run_meme()`.
`timeout`	`numeric(1)` Stop MEME program past `timeout` (seconds). See `processx::run()`.
`bin`	`character(1)` Location of MEME binary. Alternatively, set this via `options(meme.bin = '/path/to/meme/bin')`.

Value

list The output file is read with read_meme().

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Examples

## Not run: 
## To check that you are properly linking to the binary:
run_meme()

## End(Not run)

## Not run: 
## To check that you are properly linking to the binary:
run_meme()

## End(Not run)

Generate binding sites from a motif.

Description

Given probabilities for a sequence as represented by a motif, generate random sequences with the same length as the motif.

Usage

sample_sites(motif, n = 100, use.freq = 1)
sample_sites(motif, n = 100, use.freq = 1)

Arguments

`motif`	See `convert_motifs()` for acceptable formats.
`n`	`numeric(1)` Number of sites to generate.
`use.freq`	`numeric(1)` If one, use regular motif matrix. Otherwise, use respective `multifreq` matrix.

Value

XStringSet object.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

motif <- create_motif()
sites <- sample_sites(motif)

motif <- create_motif()
sites <- sample_sites(motif)

Scan sequences for matches to input motifs.

Description

For sequences of any alphabet, scan them using the PWM matrices of a set of input motifs.

Usage

scan_sequences(motifs, sequences, threshold = 1e-04,
  threshold.type = c("pvalue", "qvalue", "logodds", "logodds.abs"),
  RC = FALSE, use.freq = 1, verbose = 0, nthreads = 1,
  motif_pvalue.k = 8, use.gaps = TRUE, allow.nonfinite = FALSE,
  warn.NA = TRUE, calc.pvals = TRUE, return.granges = FALSE,
  no.overlaps = FALSE, no.overlaps.by.strand = FALSE,
  no.overlaps.strat = c("score", "order"), respect.strand = FALSE,
  motif_pvalue.method = c("dynamic", "exhaustive"),
  calc.qvals = calc.pvals, calc.qvals.method = c("fdr", "BH",
  "bonferroni"))
scan_sequences(motifs, sequences, threshold = 1e-04,
  threshold.type = c("pvalue", "qvalue", "logodds", "logodds.abs"),
  RC = FALSE, use.freq = 1, verbose = 0, nthreads = 1,
  motif_pvalue.k = 8, use.gaps = TRUE, allow.nonfinite = FALSE,
  warn.NA = TRUE, calc.pvals = TRUE, return.granges = FALSE,
  no.overlaps = FALSE, no.overlaps.by.strand = FALSE,
  no.overlaps.strat = c("score", "order"), respect.strand = FALSE,
  motif_pvalue.method = c("dynamic", "exhaustive"),
  calc.qvals = calc.pvals, calc.qvals.method = c("fdr", "BH",
  "bonferroni"))

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`sequences`	`XStringSet` Sequences to scan. Alphabet should match motif.
`threshold`	`numeric(1)` See details.
`threshold.type`	`character(1)` One of `c('pvalue', 'qvalue', 'logodds', 'logodds.abs')`. See details.
`RC`	`logical(1)` If `TRUE`, check reverse complement of the input sequences. Only available for DNA/RNA.
`use.freq`	`numeric(1)` The default, 1, uses the motif matrix (from the `motif['motif']` slot) to search for sequences. If a higher number is used, then the matching k-let matrix from the `motif['multifreq']` slot is used. See `add_multifreq()`.
`verbose`	`numeric(1)` Describe progress, from none (`0`) to verbose (`3`).
`nthreads`	`numeric(1)` Run `scan_sequences()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with only a single motif and sequence.
`motif_pvalue.k`	`numeric(1)` Control `motif_pvalue()` approximation. See `motif_pvalue()`. Only used if `motif_pvalue.method = "exhaustive"`.
`use.gaps`	`logical(1)` Set this to `FALSE` to ignore motif gaps, if present.
`allow.nonfinite`	`logical(1)` If `FALSE`, then apply a pseudocount if non-finite values are found in the PWM. Note that if the motif has a pseudocount greater than zero and the motif is not currently of type PWM, then this parameter has no effect as the pseudocount will be applied automatically when the motif is converted to a PWM internally. This value is set to `FALSE` by default in order to stay consistent with pre-version 1.8.0 behaviour. Also note that this parameter is not compatible with `motif_pvalue.method = "dynamic"`. A message will be printed if a pseudocount is applied. To disable this, set `options(pseudocount.warning=FALSE)`.
`warn.NA`	`logical(1)` Whether to warn about the presence of non-standard letters in the input sequence, such as those in masked sequences.
`calc.pvals`	`logical(1)` Calculate P-values for each hit. This is a convenience option which simply gives `motif_pvalue()` the input motifs and the scores of each hit. Be careful about setting this to `TRUE` if you anticipate getting thousands of hits and are using `motif_pvalue.method = "exhaustive"`: expect to wait a few seconds or minutes for the calculations to finish. Increasing the `nthreads` value can help greatly here. See Details for more information on P-value calculation. If `motif_pvalue.method = "dynamic"`, then this is usually not an issue.
`return.granges`	`logical(1)` Return the results as a `GRanges` object. Requires the `GenomicRanges` package to be installed.
`no.overlaps`	`logical(1)` Remove overlapping hits from the same motifs. Overlapping hits from different motifs are preserved. Please note that the current implementation of this feature can add significantly to the run time for large inputs.
`no.overlaps.by.strand`	`logical(1)` Whether to discard overlapping hits from the opposite strand (`TRUE`), or to only discard overlapping hits on the same strand (`FALSE`).
`no.overlaps.strat`	`character(1)` One of `c("score", "order")`. The former option keeps the highest scoring overlapping hit (and the first of these within ties), and the latter simply keeps the first overlapping hit.
`respect.strand`	`logical(1)` If motifs are DNA/RNA, then setting this option to `TRUE` will make `scan_sequences()` only scan the strands of the input sequences as indicated in the motif `strand` slot.
`motif_pvalue.method`	`character(1)` One of `c("dynamic", "exhaustive")`. Algorithm used for calculating P-values. The `"exhaustive"` method involves finding all possible motif matches at or above the specified score using a branch-and-bound algorithm, which can be computationally intensive (Hartman et al., 2013). Additionally, the computation must be repeated for each hit. The `"dynamic"` method calculates the distribution of possible motif scores using a much faster dynamic programming algorithm, and can be recycled for multiple scores (Grant et al., 2011). The only disadvantage is the inability to use `allow.nonfinite = TRUE`. See `motif_pvalue()` for details.
`calc.qvals`	`logical(1)` Whether to also calculate adjusted P-values. Only valid if `calc.pvals = TRUE`.
`calc.qvals.method`	`character(1)` One of `c("fdr", "BH", "bonferroni")`. The method for calculating adjusted P-values. These are described in depth in the Sequence Searches vignette. Also see Noble (2009).

Details

Logodds scoring

Similar to Biostrings::matchPWM(), the scanning method uses logodds scoring. (To see the scoring matrix for any motif, simply run convert_type(motif, "PWM"). For a multifreq scoring matrix: apply(motif["multifreq"][["2"]], 2, ppm_to_pwm)). In order to score a sequence, at each position within a sequence of length equal to the length of the motif, the scores for each base are summed. If the score sum is above the desired threshold, it is kept.

Thresholds

If threshold.type = 'logodds', then the threshold value is multiplied by the maximum possible motif scores. To calculate the maximum possible scores a motif (of type PWM) manually, run motif_score(motif, 1). If threshold.type = 'pvalue', then threshold logodds scores are generated using motif_pvalue(). Finally, if threshold.type = 'logodds.abs', then the exact values provided will be used as thresholds. Finally, if threshold.type = 'qvalue', then the threshold is calculated as if threshold.type = 'pvalue' and the final set of hits are filtered based on their calculated Q-value. (Note: this means that the thresh.score column will be incorrect!) This is done since most Q-values cannot be calculated prior to scanning. If you are running a very large job, it may be wise to use a P-value threshold followed by manually filtering by Q-value; this will avoid the scanning have to parse the larger number of hits from the internally-lowered threshold.

Non-standard letters

Non-standard letters (such as "N", "+", "-", ".", etc in DNAString objects) will be safely ignored, resulting only in a warning and a very minor performance cost. This can used to scan masked sequences. See Biostrings::mask() for masking sequences (generating MaskedXString objects), and Biostrings::injectHardMask() to recover masked XStringSet objects for use with scan_sequences(). There is also a provided wrapper function which performs both steps: mask_seqs().

Value

DataFrame, GRanges with each row representing one hit. If the input sequences are DNAStringSet or RNAStringSet, then an additional column with the strand is included. Function args are stored in the metadata slot. If return.granges = TRUE then a GRanges object is returned.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Grant CE, Bailey TL, Noble WS (2011). "FIMO: scanning for occurrences of a given motif." Bioinformatics, 27, 1017-1018.

Hartmann H, Guthohrlein EW, Siebert M, Soding SLJ (2013). “P-value-based regulatory motif discovery using positional weight matrices.” Genome Research, 23, 181-194.

Noble WS (2009). "How does multiple testing work?" Nature Biotechnology, 27, 1135-1137.

Examples

## any alphabet can be used
## Not run: 
set.seed(1)
alphabet <- paste(c(letters), collapse = "")
motif <- create_motif("hello", alphabet = alphabet)
sequences <- create_sequences(alphabet, seqnum = 1000, seqlen = 100000)
scan_sequences(motif, sequences)

## End(Not run)

## Sequence masking:
if (R.Version()$arch != "i386") {
library(Biostrings)
data(ArabidopsisMotif)
data(ArabidopsisPromoters)
seq <- mask_seqs(ArabidopsisPromoters, "AAAAA")
scan_sequences(ArabidopsisMotif, seq)
# A warning regarding the presence of non-standard letters will be given,
# but can be safely ignored in this case.
}

## any alphabet can be used
## Not run: 
set.seed(1)
alphabet <- paste(c(letters), collapse = "")
motif <- create_motif("hello", alphabet = alphabet)
sequences <- create_sequences(alphabet, seqnum = 1000, seqlen = 100000)
scan_sequences(motif, sequences)

## End(Not run)

## Sequence masking:
if (R.Version()$arch != "i386") {
library(Biostrings)
data(ArabidopsisMotif)
data(ArabidopsisPromoters)
seq <- mask_seqs(ArabidopsisPromoters, "AAAAA")
scan_sequences(ArabidopsisMotif, seq)
# A warning regarding the presence of non-standard letters will be given,
# but can be safely ignored in this case.
}

Calculate sequence complexity.

Description

Calculate sequence complexity using either the Wootton-Federhen, Trifonov, or DUST algorithms.

Usage

sequence_complexity(seqs, window.size = 20,
  window.overlap = round(window.size/2), method = c("WoottonFederhen",
  "WoottonFederhenFast", "Trifonov", "TrifonovFast", "DUST"),
  trifonov.max.word.size = 7, nthreads = 1, return.granges = FALSE)
sequence_complexity(seqs, window.size = 20,
  window.overlap = round(window.size/2), method = c("WoottonFederhen",
  "WoottonFederhenFast", "Trifonov", "TrifonovFast", "DUST"),
  trifonov.max.word.size = 7, nthreads = 1, return.granges = FALSE)

Arguments

`seqs`	`XStringSet` Input sequences.
`window.size`	`numeric` Window size. If a number between 0 and 1 is provided, the value is calculated as the number multiplied by the sequence length.
`window.overlap`	`numeric` Overlap between windows. If a number between 0 and 1 is provided, the value is calculated as the number multiplied by the sequence length.
`method`	`character(1)` Choose one of the available methods for calculating sequence complexity. See details.
`trifonov.max.word.size`	`numeric(1)` The maximum word size within each window used to calculate complexity using `method = c("Trifonov", "TrifonovFast")`. In other words, the Trifonov method involves counting the number of possible different sub-words in a window at different sizes up to the values provided by this option. It also involves calculating the product of ever increasing sequences of numbers and so in order to reduce the computations involed this can be limited to a specific maximum sub-word size.
`nthreads`	`numeric(1)` Run `sequence_complexity()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads.
`return.granges`	`logical(1)` Return the results as a `GRanges` object. Requires the `GenomicRanges` package to be installed.

Details

The Wootton-Federhen (Wootton and Federhen, 1993) and Trifonov (Trifonov, 1990) algorithms as well as their faster approximations are well described within Orlov and Potapov (2004). These algorithms score less complex sequences closer to 0, and more complex ones closer to 1. Please note that the 'fast' approximation versions of the two methods are not actually faster within sequence_complexity(), and so speed should not be a major consideration when choosing which method to use within the universalmotif package. The DUST algorithm implementation is described in Morgulis et al. (2006). In this case, less complex sequences score higher, and more complex ones closer to 0.

Briefly, the Wootton-Federhen complexity score is a reflection of the numbers of each unique letter found in the window (e.g. for DNA, the more of all four letters can be found in the window the higher the score). An increasing Trifonov score is a relection of the numbers of increasingly larger k-mers (e.g. the count of possible 1-mers, 2-mers, 3-mers, ..., until trifonov.max.word.size). Finally, the DUST score approaches 0 as the count of unique 3-mers increases. (See the final section in the examples to see how different types of sequence compositions affect the methods.)

Please note that the authors of the different methods recommend various window sizes and complexity thresholds. The authors of DUST for example, suggest using a window size of 64 and a threshold of 2 for low complexity. Wootton and Federhen suggest a window size of 40, though show that 10 and 20 can be appropriate as well (for amino acid sequences). Keep in mind however that these algorithms were implemented at a time when computers were much slower; perhaps the authors would suggest different window sizes today. One thing to note is that the Wootton-Federhen algorithm has a hard limit due to the need to caculate the product from 1:window.size. This can end up calculating values which are greater than what a double can hold (e.g. try prod(1:500)). Its approximation does not suffer from this though, as it skips calculating the product.

In terms of speed, the Wootton-Federhen algorithms are fastest, with DUST being 1-3 times slower and the Trifonov algorithms being several times slower (though the exact amount depends on the max word size).

Value

DataFrame, GRanges with each row getting a complexity score for each window in each input sequence.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Morgulis A, Gertz EM, Schaffer AA, Agarwala R (2006). "A fast and symmetric DUST implementation to mask low-complexity DNA sequences." Journal of Computational Biology, 13, 1028-1040.

Orlov YL, Potapov VN (2004). "Complexity: an internet resource for analysis of DNA sequence complexity." Nucleic Acids Research, 32, W628-W633.

Trifonov EN (1990). "Making sense of the human genome." In Sarma RH, Sarma MH (Eds), Structure & Methods Adenine Press, Albany, 1, 69-77.

Wootton JC, Federhen S (1993). "Statistics of local complexity in amino acid sequences and sequence databases." Computers & Chemistry, 17, 149-163.

Examples

## Feel free to play around with different toy sequences to get a feel for
## how the different methods perform

library(Biostrings)
test.seq <- DNAStringSet(c("AAAAAAAAAAA", "ATGACTGATGC"))

sequence_complexity(test.seq, method = "WoottonFederhen")
sequence_complexity(test.seq, method = "WoottonFederhenFast")
sequence_complexity(test.seq, method = "Trifonov")
sequence_complexity(test.seq, method = "TrifonovFast")
sequence_complexity(test.seq, method = "DUST")

## You could also use this in conjuction with mask_ranges() to hide
## low complexity regions from scanning, de novo motif discovery, etc

if (requireNamespace("GenomicRanges", quiet = TRUE)) {
data(ArabidopsisPromoters)

# Calculate complexity in 20 bp windows, sliding every 1 bp
to.mask <- sequence_complexity(ArabidopsisPromoters, method = "DUST",
  window.size = 20, window.overlap = 19, return.granges = TRUE)

# Get the ranges with a complexity score greater than 3.5
to.mask <- to.mask[to.mask$complexity > 3.5]

# See what the low complexity regions look like
ArabidopsisPromoters[IRanges::reduce(to.mask)]

# Mask them with the default '-' character:
mask_ranges(ArabidopsisPromoters, to.mask)
}

## To demonstrate how the methods work, consider:
## (These examples use the calc_complexity() utility which utilizes
## the same algorithms and works on character vectors, but lacks
## the ability to use sliding windows.)
a <- "ACGT"

# For Wootton-Federhen, it can be easily shown it is only dependent
# on the counts of individual letters (though do note that the
# original paper discusses this method in the context of amino acid
calc_complexity("AAACCCGGGTTT", alph = a)  # 0.7707
calc_complexity("AACCGGTTACGT", alph = a)  # 0.7707
calc_complexity("ACGTACGTACGT", alph = a)  # 0.7707

# As letters start to see drops in counts, the scores go down too:
calc_complexity("AAAACCCCGGGG", alph = a)  # 0.6284
calc_complexity("AAAAAACCCCCC", alph = a)  # 0.4105
calc_complexity("AAAAAAAAAACC", alph = a)  # 0.2518

# Trifonov on the other hand is greatly affected by the number
# of higher order combinations:
calc_complexity("AAACCCGGGTTT", c = "Trifonov", alph = a)  # 0.6364
calc_complexity("AACCGGTTACGT", c = "Trifonov", alph = a)  # 0.7273

# This next one may seem surprising, but it indeed scores very low.
# This is because although it has many of each individual letter,
# the number of higher order letter combinations in fact is quite
# low due to this particular repeating pattern!
calc_complexity("ACGTACGTACGT", c = "Trifonov", alph = a)  # 0.01231

# By extension, this means it scores sequences with fewer
# counts of individual letters lower too.
calc_complexity("AAAACCCCGGGG", c = "Trifonov", alph = a)  # 0.2386
calc_complexity("AAAAAACCCCCC", c = "Trifonov", alph = a)  # 0.0227
calc_complexity("AAAAAAAAAACC", c = "Trifonov", alph = a)  # 0.0011

# As for DUST, it considers the number of 3-mers in the sequence.
# The higher the numbers of 3-mers, the lower the score.
# (0 = the max possible number of DNA 3-mers for the window size)
calc_complexity("AAACCCGGGTTT", c = "DUST", alph = a)  # 0
calc_complexity("AACCGGTTACGT", c = "DUST", alph = a)  # 0
calc_complexity("ACGTACGTACGT", c = "DUST", alph = a)  # 0.8889
calc_complexity("AAAACCCCGGGG", c = "DUST", alph = a)  # 0.333
calc_complexity("ACGACGACGACG", c = "DUST", alph = a)  # 1.333
calc_complexity("AAAAAACCCCCC", c = "DUST", alph = a)  # 1.333
# Similarly to Trifonov, the next one also scores as less complex
# compared to the previous one:
calc_complexity("ACACACACACAC", c = "DUST", alph = a)  # 2.222
calc_complexity("AAAAAAAAAACC", c = "DUST", alph = a)  # 3.111
calc_complexity("AAAAAAAAAAAC", c = "DUST", alph = a)  # 4
calc_complexity("AAAAAAAAAAAA", c = "DUST", alph = a)  # 5

# Just to show once more why the seemingly more complex sequences
# such as "ACACACACACAC" score as less complex than "AAAAAACCCCCC"
# for the Trifonov and DUST methods:
count_klets("ACACACACACAC", k = 3)  # Only 2 possible 3-mers
count_klets("AAAAAACCCCCC", k = 3)  # Now 4 possible 3-mers!

## Feel free to play around with different toy sequences to get a feel for
## how the different methods perform

library(Biostrings)
test.seq <- DNAStringSet(c("AAAAAAAAAAA", "ATGACTGATGC"))

sequence_complexity(test.seq, method = "WoottonFederhen")
sequence_complexity(test.seq, method = "WoottonFederhenFast")
sequence_complexity(test.seq, method = "Trifonov")
sequence_complexity(test.seq, method = "TrifonovFast")
sequence_complexity(test.seq, method = "DUST")

## You could also use this in conjuction with mask_ranges() to hide
## low complexity regions from scanning, de novo motif discovery, etc

if (requireNamespace("GenomicRanges", quiet = TRUE)) {
data(ArabidopsisPromoters)

# Calculate complexity in 20 bp windows, sliding every 1 bp
to.mask <- sequence_complexity(ArabidopsisPromoters, method = "DUST",
  window.size = 20, window.overlap = 19, return.granges = TRUE)

# Get the ranges with a complexity score greater than 3.5
to.mask <- to.mask[to.mask$complexity > 3.5]

# See what the low complexity regions look like
ArabidopsisPromoters[IRanges::reduce(to.mask)]

# Mask them with the default '-' character:
mask_ranges(ArabidopsisPromoters, to.mask)
}

## To demonstrate how the methods work, consider:
## (These examples use the calc_complexity() utility which utilizes
## the same algorithms and works on character vectors, but lacks
## the ability to use sliding windows.)
a <- "ACGT"

# For Wootton-Federhen, it can be easily shown it is only dependent
# on the counts of individual letters (though do note that the
# original paper discusses this method in the context of amino acid
calc_complexity("AAACCCGGGTTT", alph = a)  # 0.7707
calc_complexity("AACCGGTTACGT", alph = a)  # 0.7707
calc_complexity("ACGTACGTACGT", alph = a)  # 0.7707

# As letters start to see drops in counts, the scores go down too:
calc_complexity("AAAACCCCGGGG", alph = a)  # 0.6284
calc_complexity("AAAAAACCCCCC", alph = a)  # 0.4105
calc_complexity("AAAAAAAAAACC", alph = a)  # 0.2518

# Trifonov on the other hand is greatly affected by the number
# of higher order combinations:
calc_complexity("AAACCCGGGTTT", c = "Trifonov", alph = a)  # 0.6364
calc_complexity("AACCGGTTACGT", c = "Trifonov", alph = a)  # 0.7273

# This next one may seem surprising, but it indeed scores very low.
# This is because although it has many of each individual letter,
# the number of higher order letter combinations in fact is quite
# low due to this particular repeating pattern!
calc_complexity("ACGTACGTACGT", c = "Trifonov", alph = a)  # 0.01231

# By extension, this means it scores sequences with fewer
# counts of individual letters lower too.
calc_complexity("AAAACCCCGGGG", c = "Trifonov", alph = a)  # 0.2386
calc_complexity("AAAAAACCCCCC", c = "Trifonov", alph = a)  # 0.0227
calc_complexity("AAAAAAAAAACC", c = "Trifonov", alph = a)  # 0.0011

# As for DUST, it considers the number of 3-mers in the sequence.
# The higher the numbers of 3-mers, the lower the score.
# (0 = the max possible number of DNA 3-mers for the window size)
calc_complexity("AAACCCGGGTTT", c = "DUST", alph = a)  # 0
calc_complexity("AACCGGTTACGT", c = "DUST", alph = a)  # 0
calc_complexity("ACGTACGTACGT", c = "DUST", alph = a)  # 0.8889
calc_complexity("AAAACCCCGGGG", c = "DUST", alph = a)  # 0.333
calc_complexity("ACGACGACGACG", c = "DUST", alph = a)  # 1.333
calc_complexity("AAAAAACCCCCC", c = "DUST", alph = a)  # 1.333
# Similarly to Trifonov, the next one also scores as less complex
# compared to the previous one:
calc_complexity("ACACACACACAC", c = "DUST", alph = a)  # 2.222
calc_complexity("AAAAAAAAAACC", c = "DUST", alph = a)  # 3.111
calc_complexity("AAAAAAAAAAAC", c = "DUST", alph = a)  # 4
calc_complexity("AAAAAAAAAAAA", c = "DUST", alph = a)  # 5

# Just to show once more why the seemingly more complex sequences
# such as "ACACACACACAC" score as less complex than "AAAAAACCCCCC"
# for the Trifonov and DUST methods:
count_klets("ACACACACACAC", k = 3)  # Only 2 possible 3-mers
count_klets("AAAAAACCCCCC", k = 3)  # Now 4 possible 3-mers!

Shuffle motifs by column.

Description

Given a set of motifs, shuffle the columns to create new motifs. Currently does not support keeping the 'multifreq' slot. Only the 'bkg', 'nsites', 'strand', and 'bkgsites' slots will be preserved. Uses the same shuffling methods as shuffle_sequences(). When shuffling more than one motif, all motif columns are merged into a single pool and shuffled together, finally returning them as motifs of identical lengths as the input motifs. To instead shuffle motifs individually, call shuffle_motifs() using lapply().

Usage

shuffle_motifs(motifs, k = 2, method = "linear")
shuffle_motifs(motifs, k = 2, method = "linear")

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`k`	`numeric(1)` K-let size.
`method`	`character(1)` Currently only 'linear' is accepted.

Value

Motifs. See convert_motifs() for available output formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Shuffle input sequences.

Description

Given a set of input sequences, shuffle the letters within those sequences with any k-let size.

Usage

shuffle_sequences(sequences, k = 1, method = "euler", nthreads = 1,
  rng.seed = sample.int(10000, 1), window = FALSE, window.size = 0.1,
  window.overlap = 0.01)
shuffle_sequences(sequences, k = 1, method = "euler", nthreads = 1,
  rng.seed = sample.int(10000, 1), window = FALSE, window.size = 0.1,
  window.overlap = 0.01)

Arguments

`sequences`	`XStringSet` Set of sequences to shuffle. Works with any set of characters.
`k`	`numeric(1)` K-let size.
`method`	`character(1)` One of `c('euler', 'markov', 'linear')`. Only relevant if `k > 1`. See details.
`nthreads`	`numeric(1)` Run `shuffle_sequences()` in parallel with `nthreads` threads. `nthreads = 0` uses all available threads. Note that no speed up will occur for jobs with only a single sequence.
`rng.seed`	`numeric(1)` Set random number generator seed. Since shuffling can occur simultaneously in multiple threads using C++, it cannot communicate with the regular `R` random number generator state and thus requires an independent seed. Each individual sequence in an `XStringSet` object will be given the following seed: `rng.seed * index`. The default is to pick a random number as chosen by `sample()`, which effectively is making `shuffle_sequences()` dependent on the R RNG state.
`window`	`logical(1)` Shuffle sequences iteratively over windows instead of all at once.
`window.size`	`numeric(1)` Window size. Can be a fraction less than one, or an integer representing the actual window size.
`window.overlap`	`numeric(1)` Overlap between windows. Can be a fraction less than one, or an integer representing the actual overlap size.

Details

markov method

If method = 'markov', then the Markov model is used to generate sequences which will maintain (on average) the k-let frequencies. Please note that this method is not a 'true' shuffling, and for short sequences (e.g. <100bp) this can result in slightly more dissimilar sequences versus true shuffling. See Fitch (1983) for a discussion on the topic.

euler method

If method = 'euler', then the sequence shuffling method proposed by Altschul and Erickson (1985) is used. As opposed to the 'markov' method, this one preserves exact k-let frequencies. This is done by creating a k-let edge graph, then following a random Eulerian walk through the graph. Not all walks will use up all available letters however, so the cycle-popping algorithm proposed by Propp and Wilson (1998) is used to find a random Eulerian path. A side effect of using this method is that the starting and ending sequence letters will remain unshuffled.

linear method

If method = 'linear', then the input sequences are split linearly every k letters. For example, for k = 3 'ACAGATAGACCC' becomes 'ACA GAT AGA CCC'; after which these 3-lets are shuffled randomly.

Single-letter shuffling

Do note however, that the method parameter is only relevant for k > 1. For k = 1, a simple shuffling is performed using the shuffle function from the C++ standard library.

Value

XStringSet The input sequences will be returned with identical names and lengths.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Altschul SF, Erickson BW (1985). “Significance of Nucleotide Sequence Alignments: A Method for Random Sequence Permutation That Preserves Dinucleotide and Codon Usage.” Molecular Biology and Evolution, 2, 526-538.

Fitch WM (1983). “Random sequences.” Journal of Molecular Biology, 163, 171-176.

Propp JG, Wilson DW (1998). “How to get a perfectly random sample from a generic markov chain and generate a random spanning tree of a directed graph.” Journal of Algorithms, 27, 170-217.

Examples

if (R.Version()$arch != "i386") {
sequences <- create_sequences()
sequences.shuffled <- shuffle_sequences(sequences, k = 2)
}

if (R.Version()$arch != "i386") {
sequences <- create_sequences()
sequences.shuffled <- shuffle_sequences(sequences, k = 2)
}

Switch between DNA and RNA alphabets.

Description

Convert a motif from DNA to RNA, or RNA to DNA.

Usage

switch_alph(motifs)
switch_alph(motifs)

Arguments

motifs

See convert_motifs() for acceptable formats.

Value

The DNA/RNA version of the motifs. See convert_motifs() for acceptable output formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

DNA.motif <- create_motif()
RNA.motif <- switch_alph(DNA.motif)

DNA.motif <- create_motif()
RNA.motif <- switch_alph(DNA.motif)

Tidy manipulation of motifs.

Description

Tidy manipulation of motifs.

Usage

to_df(motifs, extrainfo = TRUE)

update_motifs(motif_df, extrainfo = TRUE, force = FALSE)

to_list(motif_df, extrainfo = TRUE, force = FALSE)

requires_update(motifs, extrainfo = TRUE)
to_df(motifs, extrainfo = TRUE)

update_motifs(motif_df, extrainfo = TRUE, force = FALSE)

to_list(motif_df, extrainfo = TRUE, force = FALSE)

requires_update(motifs, extrainfo = TRUE)

Arguments

`motifs`	List of motifs.
`extrainfo`	Use the `extrainfo` slot in the tidy `data.frame`. The column names will be taken from the character vectors themselves, and unnamed elements will be assigned a unique name. To add elements to the slot, simply create new columns in the `data.frame`. Note that these will be coerced into characters. If `extrainfo` is not set to `TRUE` in `to_df()`, then the contents of the slot will not be transferred to the `data.frame`. If `extrainfo` is not set to `TRUE` in `update_motifs()` or `to_list()`, then the extra columns will be discarded.
`motif_df`	Motif `data.frame` generated by `to_df()`.
`force`	Whether to coerce non-character data types into characters for inclusion in `extrainfo`. If `force` is `FALSE` (the default), columns which are not of type "character", "numeric", or "integer" (for example, list columns, or logical values), will not be added to the motif `extrainfo` slot, but will be passed onto the returned `universalmotif_df` unchanged. Setting `force = TRUE` coerces these values into a character, adding them to the `extrainfo` slot, and updating the `universalmotif_df` columns to reflect this coercion. In other words, forcing inclusion of these data is destructive and will change the column values. Use with caution.

Details

To turn off the informative messages/warnings when printing the object to the console, set options(universalmotif_df.warning=FALSE).

Value

For to_df(): a data.frame with the exposed slots as columns.

For update_motifs(): the updated data.frame.

For requires_update(): TRUE if the motifs are out of date, FALSE if otherwise. Note that this function uses identical() to check for this, which can be quite slow for large datasets. It is usually just as fast to simply run update_motifs() in such cases.

For to_list(): a list of motifs.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Not run: 
library(universalmotif)
library(dplyr)

m <- c(create_motif(name = "motif A"), create_motif(name = "motif B"))

# Change the names of the motifs using the tidy way:
m <- m %>%
   to_df() %>%
   mutate(name = paste0(name, "-2")) %>%
   to_list()

# Add your own metadata to be stored in the extrainfo slot:
m_df <- to_df(m)
m_df$MyMetadata <- c("Info_1", "Info_2")
m <- to_list(m_df, extrainfo = TRUE)

## End(Not run)

## Not run: 
library(universalmotif)
library(dplyr)

m <- c(create_motif(name = "motif A"), create_motif(name = "motif B"))

# Change the names of the motifs using the tidy way:
m <- m %>%
   to_df() %>%
   mutate(name = paste0(name, "-2")) %>%
   to_list()

# Add your own metadata to be stored in the extrainfo slot:
m_df <- to_df(m)
m_df$MyMetadata <- c("Info_1", "Info_2")
m <- to_list(m_df, extrainfo = TRUE)

## End(Not run)

Trim motifs.

Description

Remove edges of motifs with low information content. Currently does not trim multifreq representations.

Usage

trim_motifs(motifs, min.ic = 0.25, trim.from = c("both", "left", "right"))
trim_motifs(motifs, min.ic = 0.25, trim.from = c("both", "left", "right"))

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`min.ic`	`numeric(1)` Minimum allowed information content. See `convert_type()` for a discussion on information content.
`trim.from`	`character(1)` Control the direction of trimming.

Value

Motifs See convert_motifs() for available output formats.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.trimmed <- trim_motifs(jaspar)

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
jaspar.trimmed <- trim_motifs(jaspar)

universalmotif: Motif class.

Description

Container for motif objects. See create_motif() for creating motifs as well as a more detailed description of the slots. For a brief description of available methods, see examples.

Usage

## S4 method for signature 'universalmotif'
x[i]

## S4 replacement method for signature 'universalmotif'
x[i] <- value

## S4 method for signature 'universalmotif'
initialize(.Object, name, altname, family, organism,
  motif, alphabet = "DNA", type, icscore, nsites, pseudocount = 1, bkg,
  bkgsites, consensus, strand = "+-", pval, qval, eval, multifreq, extrainfo,
  gapinfo)

## S4 method for signature 'universalmotif'
show(object)

## S4 method for signature 'universalmotif'
as.data.frame(x)

## S4 method for signature 'universalmotif'
subset(x, select)

## S4 method for signature 'universalmotif'
normalize(object)

## S4 method for signature 'universalmotif'
rowMeans(x)

## S4 method for signature 'universalmotif'
colMeans(x)

## S4 method for signature 'universalmotif'
colSums(x)

## S4 method for signature 'universalmotif'
rowSums(x)

## S4 method for signature 'universalmotif'
nrow(x)

## S4 method for signature 'universalmotif'
ncol(x)

## S4 method for signature 'universalmotif'
colnames(x)

## S4 method for signature 'universalmotif'
rownames(x)

## S4 method for signature 'universalmotif'
cbind(..., deparse.level = 0)
## S4 method for signature 'universalmotif'
x[i]

## S4 replacement method for signature 'universalmotif'
x[i] <- value

## S4 method for signature 'universalmotif'
initialize(.Object, name, altname, family, organism,
  motif, alphabet = "DNA", type, icscore, nsites, pseudocount = 1, bkg,
  bkgsites, consensus, strand = "+-", pval, qval, eval, multifreq, extrainfo,
  gapinfo)

## S4 method for signature 'universalmotif'
show(object)

## S4 method for signature 'universalmotif'
as.data.frame(x)

## S4 method for signature 'universalmotif'
subset(x, select)

## S4 method for signature 'universalmotif'
normalize(object)

## S4 method for signature 'universalmotif'
rowMeans(x)

## S4 method for signature 'universalmotif'
colMeans(x)

## S4 method for signature 'universalmotif'
colSums(x)

## S4 method for signature 'universalmotif'
rowSums(x)

## S4 method for signature 'universalmotif'
nrow(x)

## S4 method for signature 'universalmotif'
ncol(x)

## S4 method for signature 'universalmotif'
colnames(x)

## S4 method for signature 'universalmotif'
rownames(x)

## S4 method for signature 'universalmotif'
cbind(..., deparse.level = 0)

Arguments

`x`	universalmotif Motif.
`i`	`character` Slot.
`value`	Object to replace slot with.
`.Object`	universalmotif Final motif.
`name`	`character(1)` Motif name.
`altname`	`character(1)` Alternate motif name.
`family`	`character(1)` Transcription factor family.
`organism`	`character(1)` Species of origin.
`motif`	`matrix` Each column represents a position in the motif.
`alphabet`	`character(1)` One of `c('DNA', 'RNA', 'AA')`, or a combined string representing the letters.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`icscore`	`numeric(1)` Total information content. Automatically generated.
`nsites`	`numeric(1)` Number of sites the motif was constructed from.
`pseudocount`	`numeric(1)` Correction to be applied to prevent `-Inf` from appearing in PWM matrices.
`bkg`	`numeric` A vector of probabilities, each between 0 and 1. If higher order backgrounds are provided, then the elements of the vector must be named.
`bkgsites`	`numeric(1)` Total number of sites used to find the motif.
`consensus`	`character(1)` Consensus string. Automatically generated for 'DNA', 'RNA', and 'AA' alphabets.
`strand`	`character(1)` Whether the motif is specific to a certain strand.
`pval`	`numeric(1)` P-value associated with motif.
`qval`	`numeric(1)` Adjusted P-value associated with motif.
`eval`	`numeric(1)` E-value associated with motif.
`multifreq`	`list` See `add_multifreq()`.
`extrainfo`	`character` Any other extra information, represented as a named character vector.
`gapinfo`	`universalmotif_gapped(1)` Gapped motif information.
`object`	universalmotif Motif.
`select`	`numeric` Columns to keep.
`...`	universalmotif Motifs.
`deparse.level`	Unused.

Value

A motif object of class universalmotif.

Slots

name: character(1)
altname: character(1)
family: character(1)
organism: character(1)
motif: matrix
alphabet: character(1)
type: character(1)
icscore: numeric(1) Generated automatically.
nsites: numeric(1)
pseudocount: numeric(1)
bkg: numeric 0-order probabilities must be provided for all letters.
bkgsites: numeric(1)
consensus: character Generated automatically.
strand: character(1)
pval: numeric(1)
qval: numeric(1)
eval: numeric(1)
multifreq: list
extrainfo: character
gapinfo: universalmotif_gapped(1)

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## [
## Access the slots.
motif <- create_motif()
motif["motif"]
# you can also access multiple slots at once, released as a list
motif[c("motif", "name")]

## [<-
## Replace the slots.
motif["name"] <- "new name"
# some slots are protected
# motif["consensus"] <- "AAAA"  # not allowed

## c
## Assemble a list of motifs.
c(motif, motif)

## as.data.frame
## Represent a motif as a data.frame. The actual motif matrix is lost.
## Necessary for `summarise_motifs`.
as.data.frame(motif)

## subset
## Subset a motif matrix by column.
subset(motif, 3:7)  # extract motif core

## normalize
## Apply the pseudocount slot (or `1`, if the slot is set to zero) to the
## motif matrix.
motif2 <- create_motif("AAAAA", nsites = 100, pseudocount = 1)
normalize(motif2)

## rowMeans
## Calculate motif rowMeans.
rowMeans(motif)

## colMeans
## Calculate motif colMeans.
colMeans(motif)

## colSums
## Calculate motif colSums
colSums(motif)

## rowSums
## Calculate motif rowSums.
rowSums(motif)

## nrow
## Count motif rows.
nrow(motif)

## ncol
## Count motif columns.
ncol(motif)

## colnames
## Get motif colnames.
colnames(motif)

## rownames
## Get motif rownames.
rownames(motif)

## cbind
## Bind motifs together to create a new motif.
cbind(motif, motif2)

## [
## Access the slots.
motif <- create_motif()
motif["motif"]
# you can also access multiple slots at once, released as a list
motif[c("motif", "name")]

## [<-
## Replace the slots.
motif["name"] <- "new name"
# some slots are protected
# motif["consensus"] <- "AAAA"  # not allowed

## c
## Assemble a list of motifs.
c(motif, motif)

## as.data.frame
## Represent a motif as a data.frame. The actual motif matrix is lost.
## Necessary for `summarise_motifs`.
as.data.frame(motif)

## subset
## Subset a motif matrix by column.
subset(motif, 3:7)  # extract motif core

## normalize
## Apply the pseudocount slot (or `1`, if the slot is set to zero) to the
## motif matrix.
motif2 <- create_motif("AAAAA", nsites = 100, pseudocount = 1)
normalize(motif2)

## rowMeans
## Calculate motif rowMeans.
rowMeans(motif)

## colMeans
## Calculate motif colMeans.
colMeans(motif)

## colSums
## Calculate motif colSums
colSums(motif)

## rowSums
## Calculate motif rowSums.
rowSums(motif)

## nrow
## Count motif rows.
nrow(motif)

## ncol
## Count motif columns.
ncol(motif)

## colnames
## Get motif colnames.
colnames(motif)

## rownames
## Get motif rownames.
rownames(motif)

## cbind
## Bind motifs together to create a new motif.
cbind(motif, motif2)

universalmotif: Import, Modify and Export Motifs with R

Description

A collection of utility functions for working with motifs.

Utility functions.

Description

Utility functions have been split into two categories: those related to motifs ?'utils-motif', and those related to sequences ?'utils-sequence'.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Motif-related utility functions.

Description

Motif-related utility functions.

Usage

add_gap(motif, gaploc = ncol(motif)%/%2, mingap = 1, maxgap = 5)

average_ic(motifs, average = c("a.mean", "g.mean", "median", "fzt"))

compare_columns(x, y, method, bkg1 = rep(1/length(x), length(x)),
  bkg2 = rep(1/length(y), length(y)), nsites1 = 100, nsites2 = 100)

consensus_to_ppm(letter)

consensus_to_ppmAA(letter)

get_consensus(position, alphabet = "DNA", type = "PPM", pseudocount = 1)

get_consensusAA(position, type = "PPM", pseudocount = 0)

get_matches(motif, score, allow.nonfinite = FALSE)

get_scores(motif, allow.nonfinite = FALSE)

icm_to_ppm(position)

motif_range(motif, use.freq = 1, allow.nonfinite = FALSE)

motif_score(motif, threshold = c(0, 1), use.freq = 1,
  allow.nonfinite = FALSE, threshold.type = c("total", "fromzero"))

log_string_pval(pval)

pcm_to_ppm(position, pseudocount = 0)

position_icscore(position, bkg = numeric(), type = "PPM",
  pseudocount = 1, nsites = 100, relative_entropy = FALSE,
  schneider_correction = FALSE)

ppm_to_icm(position, bkg = numeric(), schneider_correction = FALSE,
  nsites = 100, relative_entropy = FALSE)

ppm_to_pcm(position, nsites = 100)

ppm_to_pwm(position, bkg = numeric(), pseudocount = 1, nsites = 100,
  smooth = TRUE)

prob_match(motif, match, allow.zero = TRUE)

prob_match_bkg(bkg, match)

pwm_to_ppm(position, bkg = numeric())

round_motif(motif, pct.tolerance = 0.05)

score_match(motif, match, allow.nonfinite = FALSE)

summarise_motifs(motifs, na.rm = TRUE)

ungap(motif, delete = FALSE)
add_gap(motif, gaploc = ncol(motif)%/%2, mingap = 1, maxgap = 5)

average_ic(motifs, average = c("a.mean", "g.mean", "median", "fzt"))

compare_columns(x, y, method, bkg1 = rep(1/length(x), length(x)),
  bkg2 = rep(1/length(y), length(y)), nsites1 = 100, nsites2 = 100)

consensus_to_ppm(letter)

consensus_to_ppmAA(letter)

get_consensus(position, alphabet = "DNA", type = "PPM", pseudocount = 1)

get_consensusAA(position, type = "PPM", pseudocount = 0)

get_matches(motif, score, allow.nonfinite = FALSE)

get_scores(motif, allow.nonfinite = FALSE)

icm_to_ppm(position)

motif_range(motif, use.freq = 1, allow.nonfinite = FALSE)

motif_score(motif, threshold = c(0, 1), use.freq = 1,
  allow.nonfinite = FALSE, threshold.type = c("total", "fromzero"))

log_string_pval(pval)

pcm_to_ppm(position, pseudocount = 0)

position_icscore(position, bkg = numeric(), type = "PPM",
  pseudocount = 1, nsites = 100, relative_entropy = FALSE,
  schneider_correction = FALSE)

ppm_to_icm(position, bkg = numeric(), schneider_correction = FALSE,
  nsites = 100, relative_entropy = FALSE)

ppm_to_pcm(position, nsites = 100)

ppm_to_pwm(position, bkg = numeric(), pseudocount = 1, nsites = 100,
  smooth = TRUE)

prob_match(motif, match, allow.zero = TRUE)

prob_match_bkg(bkg, match)

pwm_to_ppm(position, bkg = numeric())

round_motif(motif, pct.tolerance = 0.05)

score_match(motif, match, allow.nonfinite = FALSE)

summarise_motifs(motifs, na.rm = TRUE)

ungap(motif, delete = FALSE)

Arguments

`motif`	Motif object to calculate scores from, or add/remove gap, or round.
`gaploc`	`numeric` Motif gap locations. The gap occurs immediately after every position value. If missing, uses `round(ncol(motif) / 2)`.
`mingap`	`numeric` Minimum gap size. Must have one value for every location. If missing, set to 1.
`maxgap`	`numeric` Maximum gap size. Must have one value for every location. If missing, set to 5.
`motifs`	`list` A list of universalmotif motifs.
`average`	`character(1)` One of `c("a.mean", "g.mean", "median", "fzt")`. How to calculate the average motif information content.
`x`	`numeric` First column for comparison.
`y`	`numeric` Second column for comparison.
`method`	`character(1)` Column comparison metric. See `compare_motifs()` for details.
`bkg1`	`numeric` Vector of background probabilities for the first column. Only relevant if `method = "ALLR"`.
`bkg2`	`numeric` Vector of background probabilities for the second column. Only relevant if `method = "ALLR"`.
`nsites1`	`numeric(1)` Number of sites for the first column. Only relevant if `method = "ALLR"`.
`nsites2`	`numeric(1)` Number of sites for the second column. Only relevant if `method = "ALLR"`.
`letter`	`character(1)` Any DNA, RNA, or AA IUPAC letter. Ambiguity letters are accepted.
`position`	`numeric` A numeric vector representing the frequency or probability for each alphabet letter at a specific position.
`alphabet`	`character(1)` One of `c('DNA', 'RNA')`.
`type`	`character(1)` One of `⁠c('PCM', 'PPM', 'PWM' 'ICM')⁠`.
`pseudocount`	`numeric(1)` Used to prevent zeroes in motif matrix.
`score`	`numeric(1)` Logodds motif score.
`allow.nonfinite`	`logical(1)` If `FALSE`, then apply a pseudocount if non-finite values are found in the PWM. Note that if the motif has a pseudocount greater than zero and the motif is not currently of type PWM, then this parameter has no effect as the pseudocount will be applied automatically when the motif is converted to a PWM internally. This value is set to `FALSE` by default in order to stay consistent with pre-version 1.8.0 behaviour. A message will be printed if a pseudocount is applied. To disable this, set `options(pseudocount.warning=FALSE)`.
`use.freq`	`numeric(1)` Use regular motif or the respective `multifreq` representation.
`threshold`	`numeric(1)` Any number of numeric values between 0 and 1 representing score percentage.
`threshold.type`	`character` For `"total"`, a threshold of zero represents the minimum possible score. This means the range of scores that can be extracted is from the minimum to the maximum possible scores. For `"fromzero"`, a threshold of zero is a score of zero. This means the range of scores is from zero to the maximum. The `"total"` threshold type can only be used if no non-finite values are present in the PWM.
`pval`	`character(1)` String-formatted p-value.
`bkg`	`numeric` Should be the same length as the alphabet length.
`nsites`	`numeric(1)` Number of sites motif originated from.
`relative_entropy`	`logical(1)` Calculate information content as relative entropy or Kullback-Leibler divergence.
`schneider_correction`	`logical(1)` Apply sample size correction.
`smooth`	`logical(1)` Apply pseudocount correction.
`match`	`character` Sequence string to calculate score from.
`allow.zero`	`logical(1)` If `FALSE`, apply a pseudocount if zero values are found in the background frequencies.
`pct.tolerance`	`numeric(1)` or `character(1)` The minimum tolerated proportion each letter must represent per position in order not to be rounded off, either as a numeric value from 0 to 1 or a percentage written as a string from "0%" to "100%".
`na.rm`	`logical` Remove columns where all values are `NA`.
`delete`	`logical(1)` Clear gap information from motif. If `FALSE`, then it can be reactivated simply with `add_gap(motif)`.

Value

For consensus_to_ppm() and consensus_to_ppmAA(): a numeric vector of length 4 and 20, respectively.

For get_consensus() and get_consensusAA(): a character vector of length 1.

For get_matches(): a character vector of motif matches.

For motif_range(): a named numeric vector of motif scores.

For motif_score(): a named numeric vector of motif scores.

For log_string_pval(): a numeric vector of length 1.

For position_icscore(): a numeric vector of length 1.

For ppm_to_icm(), icm_to_ppm(), pcm_to_ppm(), ppm_to_pcm(), ppm_to_pwm(), and pwm_to_ppm(): a numeric vector with length equal to input numeric vector.

For prob_match(): a numeric vector of probabilities.

For round_motif(): the input motif, rounded.

For score_match(): a numeric vector with the match motif score.

For summarise_motifs(): a data.frame with columns representing the universalmotif slots.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

data(examplemotif)
examplemotif0 <- examplemotif
examplemotif0["pseudocount"] <- 0

#######################################################################
## add_gap
## Add gap information to a motif.
m <- create_motif()
# Add a gap size 5-8 between positions 4 and 5:
m <- add_gap(m, gaploc = 4, mingap = 5, maxgap = 8)

#######################################################################
## average_ic
## Calculate the average information content for a list of motifs.
m <- create_motif()
average_ic(m, "fzt")

#######################################################################
## compare_columns
## Compare two numeric vectors using the metrics from compare_motifs()
compare_columns(c(0.5, 0.1, 0.1, 0.2), c(0.7, 0.1, 0.1, 0.1), "PCC")

#######################################################################
## consensus_to_ppm
## Do the opposite of get_consensus. Note that loss of information is
## inevitable. Generates a sequence matrix.
sapply(c("A", "G", "T", "B"), consensus_to_ppm)

#######################################################################
## consensus_to_ppmAA
## Do the opposite of get_consensusAA and generate a motif matrix.
sapply(c("V", "A", "L"), consensus_to_ppmAA)

#######################################################################
## get_consensus
## Get a consensus string from a DNA/RNA motif.
m <- create_motif()["motif"]
apply(m, 2, get_consensus)

#######################################################################
## get_consensusAA
## Get a consensus string from an amino acid motif. Unless each position
## is clearly dominated by a single amino acid, the resulting string will
## likely be useless.
m <- create_motif(alphabet = "AA")["motif"]
apply(m, 2, get_consensusAA, type = "PPM")

#######################################################################
## get_match
## Get all possible motif matches above input score
get_matches(examplemotif, 0)
get_matches(examplemotif0, 0, allow.nonfinite = TRUE)

#######################################################################
## get_scores
## Get all possible scores for a motif
length(get_scores(examplemotif))
get_scores(examplemotif)
get_scores(examplemotif0, allow.nonfinite = TRUE)

#######################################################################
## icm_to_ppm
## Do the opposite of ppm_to_icm.
m <- create_motif(type = "ICM")["motif"]
apply(m, 2, icm_to_ppm)

#######################################################################
## motif_range
## Calculate the range of possible logodds scores for a motif
motif_range(examplemotif)
motif_range(examplemotif, allow.nonfinite = TRUE)

#######################################################################
## motif_score
## Calculate motif score from different thresholds
m <- normalize(examplemotif)
motif_score(m, c(0, 0.8, 1))
motif_score(examplemotif0, c(0, 0.8, 1), allow.nonfinite = TRUE,
   threshold.type = "fromzero")

#######################################################################
## log_string_pval
## Get the log of a string-formatted p-value
log_string_pval("1e-200")

#######################################################################
## pcm_to_ppm
## Go from a count type motif to a probability type motif.
m <- create_motif(type = "PCM", nsites = 50)["motif"]
apply(m, 2, pcm_to_ppm, pseudocount = 1)

#######################################################################
## position_icscore
## Similar to ppm_to_icm, except this calculates the position sum.
m <- create_motif()["motif"]
apply(m, 2, position_icscore, type = "PPM", bkg = rep(0.25, 4))

#######################################################################
## ppm_to_icm
## Convert one column from a probability type motif to an information
## content type motif.
m <- create_motif(nsites = 100, pseudocount = 0.8)["motif"]
apply(m, 2, ppm_to_icm, nsites = 100, bkg = rep(0.25, 4))

#######################################################################
## ppm_to_pcm
## Do the opposite of pcm_to_ppm.
m <- create_motif()["motif"]
apply(m, 2, ppm_to_pcm, nsites = 50)

#######################################################################
## ppm_to_pwm
## Go from a probability type motif to a weight type motif.
m <- create_motif()["motif"]
apply(m, 2, ppm_to_pwm, nsites = 100, bkg = rep(0.25, 4))

#######################################################################
## prob_match, prob_match_bkg
## Calculate probability of a particular match based on background
## frequencies
prob_match(examplemotif, "TATATAT")
## Since this motif has a uniform background, the probability of
## finding any motif hit within the sequence is equal
prob_match(examplemotif, "TATATAG")
m <- examplemotif
m["bkg"] <- c(0.3, 0.2, 0.2, 0.3)
prob_match(m, "TATATAT")
## The prob_match_bkg alternative allows you to simply pass along the
## background frequencies
prob_match_bkg(c(A=0.3, C=0.2, G=0.2, T=0.3), c("TATATAT", "TATATAG"))

#######################################################################
## pwm_to_ppm
## Do the opposite of ppm_to_pwm.
m <- create_motif(type = "PWM")["motif"]
apply(m, 2, pwm_to_ppm, bkg = rep(0.25, 4))

#######################################################################
## Note that not all type conversions can be done directly; for those
## type conversions which are unavailable, universalmotif just chains
## together others (i.e. from PCM -> ICM => pcm_to_ppm -> ppm_to_icm)

#######################################################################
## round_motif
## Round down letter scores to 0
m <- create_motif()
## Remove letters from positions which are less than 5% of the total
## position:
round_motif(m, pct.tolerance = 0.05)

#######################################################################
## score_match
## Calculate score of a particular match
score_match(examplemotif, "TATATAT")
score_match(examplemotif, "TATATAG")
score_match(examplemotif0, "TATATAT", allow.nonfinite = TRUE)
score_match(examplemotif0, "TATATAG", allow.nonfinite = TRUE)

#######################################################################
## summarise_motifs
## Create a data.frame of information based on a list of motifs.
m1 <- create_motif()
m2 <- create_motif()
m3 <- create_motif()
summarise_motifs(list(m1, m2, m3))

#######################################################################
## ungap
## Unset motif's gap status. Does not delete actual gap data unless
## delete = TRUE.
m <- create_motif()
m <- add_gap(m, 3, 2, 4)
m <- ungap(m)
# Restore gap data:
m <- add_gap(m)

data(examplemotif)
examplemotif0 <- examplemotif
examplemotif0["pseudocount"] <- 0

#######################################################################
## add_gap
## Add gap information to a motif.
m <- create_motif()
# Add a gap size 5-8 between positions 4 and 5:
m <- add_gap(m, gaploc = 4, mingap = 5, maxgap = 8)

#######################################################################
## average_ic
## Calculate the average information content for a list of motifs.
m <- create_motif()
average_ic(m, "fzt")

#######################################################################
## compare_columns
## Compare two numeric vectors using the metrics from compare_motifs()
compare_columns(c(0.5, 0.1, 0.1, 0.2), c(0.7, 0.1, 0.1, 0.1), "PCC")

#######################################################################
## consensus_to_ppm
## Do the opposite of get_consensus. Note that loss of information is
## inevitable. Generates a sequence matrix.
sapply(c("A", "G", "T", "B"), consensus_to_ppm)

#######################################################################
## consensus_to_ppmAA
## Do the opposite of get_consensusAA and generate a motif matrix.
sapply(c("V", "A", "L"), consensus_to_ppmAA)

#######################################################################
## get_consensus
## Get a consensus string from a DNA/RNA motif.
m <- create_motif()["motif"]
apply(m, 2, get_consensus)

#######################################################################
## get_consensusAA
## Get a consensus string from an amino acid motif. Unless each position
## is clearly dominated by a single amino acid, the resulting string will
## likely be useless.
m <- create_motif(alphabet = "AA")["motif"]
apply(m, 2, get_consensusAA, type = "PPM")

#######################################################################
## get_match
## Get all possible motif matches above input score
get_matches(examplemotif, 0)
get_matches(examplemotif0, 0, allow.nonfinite = TRUE)

#######################################################################
## get_scores
## Get all possible scores for a motif
length(get_scores(examplemotif))
get_scores(examplemotif)
get_scores(examplemotif0, allow.nonfinite = TRUE)

#######################################################################
## icm_to_ppm
## Do the opposite of ppm_to_icm.
m <- create_motif(type = "ICM")["motif"]
apply(m, 2, icm_to_ppm)

#######################################################################
## motif_range
## Calculate the range of possible logodds scores for a motif
motif_range(examplemotif)
motif_range(examplemotif, allow.nonfinite = TRUE)

#######################################################################
## motif_score
## Calculate motif score from different thresholds
m <- normalize(examplemotif)
motif_score(m, c(0, 0.8, 1))
motif_score(examplemotif0, c(0, 0.8, 1), allow.nonfinite = TRUE,
   threshold.type = "fromzero")

#######################################################################
## log_string_pval
## Get the log of a string-formatted p-value
log_string_pval("1e-200")

#######################################################################
## pcm_to_ppm
## Go from a count type motif to a probability type motif.
m <- create_motif(type = "PCM", nsites = 50)["motif"]
apply(m, 2, pcm_to_ppm, pseudocount = 1)

#######################################################################
## position_icscore
## Similar to ppm_to_icm, except this calculates the position sum.
m <- create_motif()["motif"]
apply(m, 2, position_icscore, type = "PPM", bkg = rep(0.25, 4))

#######################################################################
## ppm_to_icm
## Convert one column from a probability type motif to an information
## content type motif.
m <- create_motif(nsites = 100, pseudocount = 0.8)["motif"]
apply(m, 2, ppm_to_icm, nsites = 100, bkg = rep(0.25, 4))

#######################################################################
## ppm_to_pcm
## Do the opposite of pcm_to_ppm.
m <- create_motif()["motif"]
apply(m, 2, ppm_to_pcm, nsites = 50)

#######################################################################
## ppm_to_pwm
## Go from a probability type motif to a weight type motif.
m <- create_motif()["motif"]
apply(m, 2, ppm_to_pwm, nsites = 100, bkg = rep(0.25, 4))

#######################################################################
## prob_match, prob_match_bkg
## Calculate probability of a particular match based on background
## frequencies
prob_match(examplemotif, "TATATAT")
## Since this motif has a uniform background, the probability of
## finding any motif hit within the sequence is equal
prob_match(examplemotif, "TATATAG")
m <- examplemotif
m["bkg"] <- c(0.3, 0.2, 0.2, 0.3)
prob_match(m, "TATATAT")
## The prob_match_bkg alternative allows you to simply pass along the
## background frequencies
prob_match_bkg(c(A=0.3, C=0.2, G=0.2, T=0.3), c("TATATAT", "TATATAG"))

#######################################################################
## pwm_to_ppm
## Do the opposite of ppm_to_pwm.
m <- create_motif(type = "PWM")["motif"]
apply(m, 2, pwm_to_ppm, bkg = rep(0.25, 4))

#######################################################################
## Note that not all type conversions can be done directly; for those
## type conversions which are unavailable, universalmotif just chains
## together others (i.e. from PCM -> ICM => pcm_to_ppm -> ppm_to_icm)

#######################################################################
## round_motif
## Round down letter scores to 0
m <- create_motif()
## Remove letters from positions which are less than 5% of the total
## position:
round_motif(m, pct.tolerance = 0.05)

#######################################################################
## score_match
## Calculate score of a particular match
score_match(examplemotif, "TATATAT")
score_match(examplemotif, "TATATAG")
score_match(examplemotif0, "TATATAT", allow.nonfinite = TRUE)
score_match(examplemotif0, "TATATAG", allow.nonfinite = TRUE)

#######################################################################
## summarise_motifs
## Create a data.frame of information based on a list of motifs.
m1 <- create_motif()
m2 <- create_motif()
m3 <- create_motif()
summarise_motifs(list(m1, m2, m3))

#######################################################################
## ungap
## Unset motif's gap status. Does not delete actual gap data unless
## delete = TRUE.
m <- create_motif()
m <- add_gap(m, 3, 2, 4)
m <- ungap(m)
# Restore gap data:
m <- add_gap(m)

Sequence-related utility functions.

Description

Sequence-related utility functions.

Usage

calc_complexity(string, complexity.method = c("WoottonFederhen",
  "WoottonFederhenFast", "Trifonov", "TrifonovFast", "DUST"), alph = NULL,
  trifonov.max.word.size = 7)

calc_windows(n, window = 1, overlap = 0, return.incomp = TRUE)

count_klets(string, k = 1, alph)

get_klets(lets, k = 1)

mask_ranges(seqs, ranges, letter = "-")

mask_seqs(seqs, pattern, RC = FALSE, letter = "-")

meme_alph(core, file = stdout(), complements = NULL, ambiguity = NULL,
  like = NULL, alph.name = NULL, letter.names = NULL, colours = NULL)

shuffle_string(string, k = 1, method = c("euler", "linear", "markov"),
  rng.seed = sample.int(10000, 1))

slide_fun(string, FUN, FUN.VALUE, window = 1, overlap = 0,
  return.incomp = TRUE)

window_string(string, window = 1, overlap = 0, return.incomp = TRUE,
  nthreads = 1)
calc_complexity(string, complexity.method = c("WoottonFederhen",
  "WoottonFederhenFast", "Trifonov", "TrifonovFast", "DUST"), alph = NULL,
  trifonov.max.word.size = 7)

calc_windows(n, window = 1, overlap = 0, return.incomp = TRUE)

count_klets(string, k = 1, alph)

get_klets(lets, k = 1)

mask_ranges(seqs, ranges, letter = "-")

mask_seqs(seqs, pattern, RC = FALSE, letter = "-")

meme_alph(core, file = stdout(), complements = NULL, ambiguity = NULL,
  like = NULL, alph.name = NULL, letter.names = NULL, colours = NULL)

shuffle_string(string, k = 1, method = c("euler", "linear", "markov"),
  rng.seed = sample.int(10000, 1))

slide_fun(string, FUN, FUN.VALUE, window = 1, overlap = 0,
  return.incomp = TRUE)

window_string(string, window = 1, overlap = 0, return.incomp = TRUE,
  nthreads = 1)

Arguments

`string`	`character(1)` A character vector containing a single string, with the exception of `calc_complexity()` where `string` can be a length greater than one.
`complexity.method`	`character(1)` Complexity algorithm. See `sequence_complexity()`.
`alph`	`character(1)` A single character string with the desired sequence alphabet. If missing, finds the unique letters within each string.
`trifonov.max.word.size`	`integer(1)` Maximum word size for use in the Trifonov complexity methods. See `sequence_complexity()`.
`n`	`integer(1)` Total size from which to calculate sliding windows.
`window`	`integer(1)` Window size to slide along.
`overlap`	`integer(1)` Overlap size between windows.
`return.incomp`	`logical(1)` Whether to return the last window if it is smaller then the requested window size.
`k`	`integer(1)` K-let size.
`lets`	`character` A character vector where each element will be considered a single unit.
`seqs`	`XStringSet` Sequences to mask. Cannot be `BStringSet`.
`ranges`	`GRanges` The ranges to mask. Must be a `GRanges` object from the `GenomicRanges` package.
`letter`	`character(1)` Character to use for masking.
`pattern`	`character(1)` Pattern to mask.
`RC`	`logical(1)` Whether to mask the reverse complement of the pattern.
`core`	`character(1)` Core alphabet symbols. If complements are also provided, then only half of the letters should be provided to this argument.
`file`	Output file.
`complements`	`character(1)`, `NULL` Complementary letters to the core symbols.
`ambiguity`	`character(1)`, `NULL` A named vector providing ambiguity codes for the custom alphabet.
`like`	`character(1)`, `NULL` How to classify the custom alphabet. If not `NULL`, then one of `c("DNA", "RNA", "PROTEIN")`.
`alph.name`	`character(1)`, `NULL` Custom alphabet name.
`letter.names`	`character`, `NULL` Named vector of core symbol names.
`colours`	`character`, `NULL` Named vector of core symbol colours. MEME requires hex colours.
`method`	`character(1)` Shuffling method. One of `c("euler", "linear", "markov")`. See `shuffle_sequences()`.
`rng.seed`	`numeric(1)` Set random number generator seed. Since shuffling in `shuffle_sequences()` can occur simultaneously in multiple threads using C++, it cannot communicate with the regular `R` random number generator state and thus requires an independent seed. Since `shuffle_string()` uses the same underlying code as `shuffle_sequences()`, it also requires a separate seed even if it is run in serial.
`FUN`	`closure` The function to apply per window. (See `?vapply`.)
`FUN.VALUE`	The expected return type for `FUN`. (See `?vapply`.)
`nthreads`	`integer(1)` Number of threads to use. Zero uses all available threads.

Value

For calc_complexity(): A vector of numeric values.

For calc_windows(): A data.frame with columns start and stop.

For count_klets(): A data.frame with columns lets and counts.

For get_klets(): A character vector of k-lets.

For mask_ranges(): The masked XStringSet object.

For mask_seqs(): The masked XStringSet object.

For meme_alph(): NULL, invisibly.

For shuffle_string(): A single character string.

For slide_fun(): A vector with type FUN.VALUE.

For window_string(): A character vector.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

#######################################################################
## calc_complexity
## Calculate complexity for abitrary strings
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "WoottonFederhen")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "WoottonFederhenFast")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "Trifonov")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "TrifonovFast")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "DUST")

#######################################################################
## calc_windows
## Calculate window coordinates for any value 'n'.
calc_windows(100, 10, 5)

#######################################################################
## count_klets
## Count k-lets for any string of characters
count_klets("GCAAATGTACGCAGGGCCGA", k = 2)
## The default 'k' value (1) counts individual letters
count_klets("GCAAATGTACGCAGGGCCGA")

#######################################################################
## get_klets
## Generate all possible k-lets for a set of characters
get_klets(c("A", "C", "G", "T"), 3)
## Note that each element in 'lets' is considered a single unit;
## see:
get_klets(c("AA", "B"), k = 2)

#######################################################################
## mask_ranges
## Mask arbitrary ranges
if (requireNamespace("GenomicRanges", quiet = TRUE)) {
ranges <- GenomicRanges::GRanges("A", IRanges::IRanges(1, 5))
seq <- Biostrings::DNAStringSet(c(A = "ATGACTGATTACTTATA"))
mask_ranges(seq, ranges, "-")
}

#######################################################################
## mask_seqs
## Mask repetitive seqeuences
data(ArabidopsisPromoters)
mask_seqs(ArabidopsisPromoters, "AAAAAA")

#######################################################################
## meme_alph
## Create MEME custom alphabet definition files
meme_alph("ACm", complements = "TGM", alph.name = "MethDNA",
  letter.names = c(A = "Adenine", C = "Cytosine", G = "Guanine",
    T = "Thymine", m = "Methylcytosine", M = "mC:Guanine"),
  like = "DNA", ambiguity = c(N = "ACGTmM"))

#######################################################################
## shuffle_string
## Shuffle any string of characters
shuffle_string("ASDADASDASDASD", k = 1)

#######################################################################
## slide_fun
## Apply a function to a character vector along sliding windows
FUN <- function(x) grepl("[GC]", x)
data.frame(
  Window = window_string("ATGCATCTATGCA", 2, 1),
  HasGC = slide_fun("ATGCATCTATGCA", FUN, logical(1), 2, 1)
)

#######################################################################
## window_string
## Get sliding windows for a string of characters
window_string("ABCDEFGHIJ", 2, 1)

#######################################################################
## calc_complexity
## Calculate complexity for abitrary strings
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "WoottonFederhen")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "WoottonFederhenFast")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "Trifonov")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "TrifonovFast")
calc_complexity("GTGCCCCGCGGGAACCCCGC", c = "DUST")

#######################################################################
## calc_windows
## Calculate window coordinates for any value 'n'.
calc_windows(100, 10, 5)

#######################################################################
## count_klets
## Count k-lets for any string of characters
count_klets("GCAAATGTACGCAGGGCCGA", k = 2)
## The default 'k' value (1) counts individual letters
count_klets("GCAAATGTACGCAGGGCCGA")

#######################################################################
## get_klets
## Generate all possible k-lets for a set of characters
get_klets(c("A", "C", "G", "T"), 3)
## Note that each element in 'lets' is considered a single unit;
## see:
get_klets(c("AA", "B"), k = 2)

#######################################################################
## mask_ranges
## Mask arbitrary ranges
if (requireNamespace("GenomicRanges", quiet = TRUE)) {
ranges <- GenomicRanges::GRanges("A", IRanges::IRanges(1, 5))
seq <- Biostrings::DNAStringSet(c(A = "ATGACTGATTACTTATA"))
mask_ranges(seq, ranges, "-")
}

#######################################################################
## mask_seqs
## Mask repetitive seqeuences
data(ArabidopsisPromoters)
mask_seqs(ArabidopsisPromoters, "AAAAAA")

#######################################################################
## meme_alph
## Create MEME custom alphabet definition files
meme_alph("ACm", complements = "TGM", alph.name = "MethDNA",
  letter.names = c(A = "Adenine", C = "Cytosine", G = "Guanine",
    T = "Thymine", m = "Methylcytosine", M = "mC:Guanine"),
  like = "DNA", ambiguity = c(N = "ACGTmM"))

#######################################################################
## shuffle_string
## Shuffle any string of characters
shuffle_string("ASDADASDASDASD", k = 1)

#######################################################################
## slide_fun
## Apply a function to a character vector along sliding windows
FUN <- function(x) grepl("[GC]", x)
data.frame(
  Window = window_string("ATGCATCTATGCA", 2, 1),
  HasGC = slide_fun("ATGCATCTATGCA", FUN, logical(1), 2, 1)
)

#######################################################################
## window_string
## Get sliding windows for a string of characters
window_string("ABCDEFGHIJ", 2, 1)

Plot logos from numeric matrices.

Description

This function provides the plotting capabilities of view_motifs() without requiring universalmotif-class objects. Instead, it takes a numeric matrix with row names as input. Additionally, columns can be of any height and letters can be a mix of different character lengths.

Usage

view_logo(x, fontDF = NULL, fill = "black", colour.scheme = NULL,
  min.height = 0.01, x.spacer = 0.04, y.spacer = 0.01,
  sort.positions = FALSE, sort.positions.decreasing = TRUE,
  fit.to.height = NULL)
view_logo(x, fontDF = NULL, fill = "black", colour.scheme = NULL,
  min.height = 0.01, x.spacer = 0.04, y.spacer = 0.01,
  sort.positions = FALSE, sort.positions.decreasing = TRUE,
  fit.to.height = NULL)

Arguments

`x`	A numeric matrix with row names. The row names can be a mix of different character lengths.
`fontDF`	`data.frame` or `DataFrame` Polygon data for letters used for plotting, as generated by the `createPolygons()` function from the `gglogo` package. See the `fontDFroboto` data object (which is used by default when `fontDF = NULL`). See `Examples` for how to generate your own font set. Expected columns: `x`, `y`, `order`, `group`; additional columns will be ignored.
`fill`	`character` A single colour to fill all letters with. Ignored if `colour.scheme` is provided.
`colour.scheme`	`character` A named character vector of colour names. Provide colours for individual letters, even if the row names are made up of multiple characters.
`min.height`	`numeric(1)` Minimum height for a letter to be plotted. The number is taken as the fraction of the total height of the plot. The default value is to not show letters which take up 1% or less of the vertical space. For smaller figures it is recommended to increase this value, and vice versa for larger figures.
`x.spacer`	`numeric(1)` Add horizontal spacing between letters. The number is taken as the fraction of the width of an individual position. Increasing this value is recommended for letters made up of multiple characters.
`y.spacer`	`numeric(1)` Add vertical spacing between letters. The number is taken as the fraction nof the total height of the plot.
`sort.positions`	`logical(1)` Sort letters vertically per position by height.
`sort.positions.decreasing`	`logical(1)` Sort in decreasing or increasing order based on letter height.
`fit.to.height`	`numeric(1)` Normalize the per position height to this value. If `NULL`, no normalization is applied. Note that this parameter is ignored if `use.type = c("PWM", "ICM")`.

Value

A ggplot object. If you wish to plot the data yourself from polygon paths, access them using ⁠$data⁠ on the output object. The theme theme_void() is applied to the object; apply your own theme or adjust specific plot parameters with theme() to change this.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Feel free to mix and match row name character lengths and column sums.
data(examplemotif)
toplot <- examplemotif["motif"]
toplot[4] <- 2
toplot[20] <- -0.5
rownames(toplot)[1] <- "AA"
view_logo(toplot)

## Feel free to mix and match row name character lengths and column sums.
data(examplemotif)
toplot <- examplemotif["motif"]
toplot[4] <- 2
toplot[20] <- -0.5
rownames(toplot)[1] <- "AA"
view_logo(toplot)

Plot motif logos.

Description

Show sequence logo. If given a list of more than one motif, then the motifs are aligned with the first in the list.

Usage

view_motifs(motifs, use.type = "ICM", method = "ALLR", tryRC = TRUE,
  min.overlap = 6, min.mean.ic = 0.25, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  return.raw = FALSE, dedup.names = TRUE, show.positions = TRUE,
  show.positions.once = TRUE, show.names = TRUE, names.pos = c("top",
  "right"), use.freq = 1, colour.scheme = NULL, fontDF = NULL,
  min.height = 0.01, x.spacer = if (use.freq == 1) 0.04 else 0.1,
  y.spacer = 0.01, sort.positions = !use.type %in% c("PCM", "PPM"),
  sort.positions.decreasing = TRUE, text.size = 16, fit.to.height = if
  (use.type == "PPM") 1 else NULL, RC.text = " [RC]", ...)
view_motifs(motifs, use.type = "ICM", method = "ALLR", tryRC = TRUE,
  min.overlap = 6, min.mean.ic = 0.25, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  return.raw = FALSE, dedup.names = TRUE, show.positions = TRUE,
  show.positions.once = TRUE, show.names = TRUE, names.pos = c("top",
  "right"), use.freq = 1, colour.scheme = NULL, fontDF = NULL,
  min.height = 0.01, x.spacer = if (use.freq == 1) 0.04 else 0.1,
  y.spacer = 0.01, sort.positions = !use.type %in% c("PCM", "PPM"),
  sort.positions.decreasing = TRUE, text.size = 16, fit.to.height = if
  (use.type == "PPM") 1 else NULL, RC.text = " [RC]", ...)

Arguments

`motifs`	See `convert_motifs()` for acceptable motif formats.
`use.type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`method`	`character(1)` One of PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
`return.raw`	`logical(1)` Instead of returning a plot, return the aligned named matrices used to generate the plot. This can be useful if you wish to use `view_motifs()` alignment capabilities for custom plotting uses. Alignment is performed by adding empty columns to the left or right of motifs to generate matrices of equal length.
`dedup.names`	`logical(1)` Plotting motifs with duplicated names is not allowed. Setting this to `TRUE` allows the names to be modified for plotting.
`show.positions`	`logical(1)` Show x-axis position tick labels.
`show.positions.once`	`logical(1)` When plotting multiple motifs, show x-axis position tick labels only once. If `FALSE`, then x-axis tick labels are specific to each motif.
`show.names`	`logical(1)` Add motif names when plotting multiple motifs.
`names.pos`	`character(1)` Motif name locations. Either above (`top`) or to the right (`right`) of the logos.
`use.freq`	`numeric(1)` Plot higher order motifs from the `multifreq` slot.
`colour.scheme`	`character` A named character vector of colour names. Default colours are provided for DNA, RNA, and AA motifs if left `NULL`.
`fontDF`	`data.frame` or `DataFrame` Polygon data for letters used for plotting, as generated by the `createPolygons()` function from the `gglogo` package. See the `fontDFroboto` data object (which is used by default when `fontDF = NULL`). See `Examples` for how to generate your own font set. Expected columns: `x`, `y`, `order`, `group`; additional columns will be ignored.
`min.height`	`numeric(1)` Minimum height for a letter to be plotted. The number is taken as the fraction of the total height of the plot. The default value is to not show letters which take up 1% or less of the vertical space. For smaller figures it is recommended to increase this value, and vice versa for larger figures.
`x.spacer`	`numeric(1)` Add horizontal spacing between letters. The number is taken as the fraction of the width of an individual position. Increasing this value is recommended for plotting multifreq motifs.
`y.spacer`	`numeric(1)` Add vertical spacing between letters. The number is taken as the fraction nof the total height of the plot.
`sort.positions`	`logical(1)` Sort letters vertically per position by height.
`sort.positions.decreasing`	`logical(1)` Sort in decreasing or increasing order based on letter height.
`text.size`	`numeric(1)` Text size for labels.
`fit.to.height`	`numeric(1)` Normalize the per position height to this value. If `NULL`, no normalization is applied. Note that this parameter is ignored if `use.type = c("PWM", "ICM")`.
`RC.text`	`character(1)` The text to display alongside the name of motifs shown as their reverse complement.
`...`	Unused. Was previously in place to allow extra args to be given to `ggseqlogo::ggseqlogo`, however `universalmotif` now implements its own motif plotting code directly with `ggplot2`.

Details

See compare_motifs() for more info on comparison parameters.

See view_logo() to plot from a numeric matrix with arbitrary values instead of a motif object.

Note: score.strat = "a.mean" is NOT recommended, as view_motifs() will not discriminate between two alignments with equal mean scores, even if one alignment is longer than the other.

Note: if you want to plot the motifs yourself, you can set return.raw=TRUE to get the numeric motif matrices and calculate the polygon paths on your own or access the polygon path data directly from the final ggplot object using ⁠$data⁠.

Value

A ggplot object. If return.raw = TRUE, a list of matrices.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

## Plotting multifreq motifs:
data(examplemotif2)
view_motifs(examplemotif2, use.freq = 2)

## Generate your own letter set:
## Not run: 

library(gglogo)  # install from CRAN first if needed
fontDFtimes <- createPolygons(LETTERS, "Times", 800, scale = TRUE)
view_motifs(examplemotif2, fontDF = fontDFtimes)

## Note: setting `scale = TRUE` is necessary to properly align letters
## vertically, but this has the effect of horizontally stretching out
## letters which shouldn't be stretched (such as "I"). If you need to plot
## letters which have been badly horizontally scaled, you can fix them
## manually as demonstrated here:

# Retrieve the x-coordinates for the desired letter:
tofix <- fontDFtimes$x[fontDFtimes$group == "I"]
# Scale the letter x-coordinates:
tofix <- tofix * 0.35
# Remember to center the letter around 0.5 again:
tofix <- tofix + (1 - max(tofix)) / 2
# Apply the fix:
fontDFtimes$x[fontDFtimes$group == "I"] <- tofix
view_motifs(create_motif("AIG", alphabet = "AA"), fontDF = fontDFtimes)


## End(Not run)

## Plotting multifreq motifs:
data(examplemotif2)
view_motifs(examplemotif2, use.freq = 2)

## Generate your own letter set:
## Not run: 

library(gglogo)  # install from CRAN first if needed
fontDFtimes <- createPolygons(LETTERS, "Times", 800, scale = TRUE)
view_motifs(examplemotif2, fontDF = fontDFtimes)

## Note: setting `scale = TRUE` is necessary to properly align letters
## vertically, but this has the effect of horizontally stretching out
## letters which shouldn't be stretched (such as "I"). If you need to plot
## letters which have been badly horizontally scaled, you can fix them
## manually as demonstrated here:

# Retrieve the x-coordinates for the desired letter:
tofix <- fontDFtimes$x[fontDFtimes$group == "I"]
# Scale the letter x-coordinates:
tofix <- tofix * 0.35
# Remember to center the letter around 0.5 again:
tofix <- tofix + (1 - max(tofix)) / 2
# Apply the fix:
fontDFtimes$x[fontDFtimes$group == "I"] <- tofix
view_motifs(create_motif("AIG", alphabet = "AA"), fontDF = fontDFtimes)


## End(Not run)

Export motifs in HOMER format.

Description

Convert DNA motifs to HOMER format and write to file. See http://homer.ucsd.edu/homer/motif/.

Usage

write_homer(motifs, file, logodds_threshold = NULL, overwrite = FALSE,
  append = FALSE, threshold = 0.8, threshold.type = c("logodds",
  "logodds.abs", "pvalue"))
write_homer(motifs, file, logodds_threshold = NULL, overwrite = FALSE,
  append = FALSE, threshold = 0.8, threshold.type = c("logodds",
  "logodds.abs", "pvalue"))

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`logodds_threshold`	Deprecated. If set, `read_homer()` will behave like pre-version 1.12.0 of the `universalmotif` package for backwards compatibility (though a warning will be printed).
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file.
`threshold`	`numeric(1)` Stringency required for HOMER to match a motif. See `scan_sequences()` for how to use this argument. Can be a single value to be recycled for all motifs, or a vector of equal length to the number of motifs.
`threshold.type`	`character(1)` How the `threshold` value should be used to obtain the final threshold value in the written motif. See `scan_sequences()` for how to use this.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Examples

motif <- create_motif()
write_homer(motif, tempfile())

motif <- create_motif()
write_homer(motif, tempfile())

Export motifs in JASPAR format.

Description

Convert motifs to JASPAR format and write to file. See http://jaspar.genereg.net/.

Usage

write_jaspar(motifs, file, overwrite = FALSE, append = FALSE)
write_jaspar(motifs, file, overwrite = FALSE, append = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Examples

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                    package = "universalmotif"))
write_jaspar(transfac, tempfile())

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                    package = "universalmotif"))
write_jaspar(transfac, tempfile())

Export motifs as raw matrices.

Description

Write motifs as simple matrices with optional headers to file.

Usage

write_matrix(motifs, file, positions = "columns", rownames = FALSE, type,
  sep = "", headers = TRUE, overwrite = FALSE, append = FALSE,
  digits = 6)
write_matrix(motifs, file, positions = "columns", rownames = FALSE, type,
  sep = "", headers = TRUE, overwrite = FALSE, append = FALSE,
  digits = 6)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`positions`	`character(1)` One of `c('columns', 'rows')`. Partial matching allowed.
`rownames`	`logical(1)` Include alphabet letters as rownames.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`. If missing will use whatever type the motif is currently stored as.
`sep`	`character(1)` Indicates how to separate individual motifs. Set as `NULL` to have no seperating lines between motifs (the default is to use a blank line).
`headers`	`logical(1)`, `character(1)` Indicating if and how to write names.
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file.
`digits`	`numeric(1)` Number of digits to use for motif positions.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Examples

motif <- create_motif()
write_matrix(motif, tempfile(), headers = ">")

motif <- create_motif()
write_matrix(motif, tempfile(), headers = ">")

Export motifs in MEME format.

Description

Convert motifs to minimal MEME format and write to file. See http://meme-suite.org/doc/meme-format.html.

Usage

write_meme(motifs, file, version = 5, bkg, strand, overwrite = FALSE,
  append = FALSE)
write_meme(motifs, file, version = 5, bkg, strand, overwrite = FALSE,
  append = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`version`	`numeric(1)` MEME version.
`bkg`	`numeric` Background letter frequencies. If missing, will use background frequencies from motif objects (if they are identical); else background frequencies will be set to freq = 1/length(alphabet)
`strand`	`character` If missing, will use strand from motif objects (if identical); otherwise will default to "+ -"
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file. Motifs will be written in minimal format, so it is recommended to only use this if the existing file is also a minimal MEME format file.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009). “MEME SUITE: tools for motif discovery and searching.” Nucleic Acids Research, 37, W202-W208.

Examples

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                    package = "universalmotif"))
write_meme(transfac, tempfile())

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                    package = "universalmotif"))
write_meme(transfac, tempfile())

Export motifs in universalmotif format.

Description

Write motifs as universalmotif objects to file. For optimal storage of universalmotif class motifs, consider using saveRDS() and readRDS(). Currently the universalmotif format is YAML-based, but this is subject to change.

Usage

write_motifs(motifs, file, minimal = FALSE, multifreq = TRUE,
  progress = FALSE, overwrite = FALSE, append = FALSE, BP = FALSE)
write_motifs(motifs, file, minimal = FALSE, multifreq = TRUE,
  progress = FALSE, overwrite = FALSE, append = FALSE, BP = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`minimal`	`logical(1)` Only write essential motif information.
`multifreq`	`logical(1)` Write `multifreq` slot, if present.
`progress`	`logical(1)` Show progress.
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing motif file. Package version in existing motif file must be greater than 1.2.0.
`BP`	`logical(1)` Allows for the use of BiocParallel within `write_motifs()`. See `BiocParallel::register()` to change the default backend.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

Export motifs in TRANSFAC format.

Description

Convert motifs to TRANSFAC format and write to file.

Usage

write_transfac(motifs, file, overwrite = FALSE, append = FALSE,
  name.tag = "ID", altname.tag = "NA")
write_transfac(motifs, file, overwrite = FALSE, append = FALSE,
  name.tag = "ID", altname.tag = "NA")

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file.
`name.tag`	`character(1)` The tag to use when writing the motifs name slot.
`altname.tag`	`character(1)` The tag to use when writing the motifs altname slot. Note that no tag will be written if the slot is empty.

Details

If the family slot of a motif is not empty, then its contents will included using the HC tag. Similarly for the organism slot using the tag OS. The default name and alternate name tags are ID and NA, respectively, though these can be set manually.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, [email protected]

References

Wingender E, Dietze P, Karas H, Knuppel R (1996). “TRANSFAC: A Database on Transcription Factors and Their DNA Binding Sites.” Nucleic Acids Research, 24, 238-241.

Examples

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                    package = "universalmotif"))
write_transfac(jaspar, tempfile())

jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                    package = "universalmotif"))
write_transfac(jaspar, tempfile())

Package 'universalmotif'

Help Index

Add multi-letter information to a motif.

Description

Usage

Arguments

Details

A note on motif size

Value

Author(s)

See Also

Examples

Arabidopsis motif in universalmotif format.

Description

Usage

Format

Arabidopsis promoters as a DNAStringSet.

Description

Usage

Format

Compare motifs.

Description

Usage

Arguments

Details

Available metrics

Calculating P-values

Value

Author(s)

References

See Also

Examples

Convert motif class.

Description

Usage

Arguments

Details

Input

Output

Value

Methods (by class)

Author(s)

References

Examples

Convert universalmotif type.

Description

Usage

Arguments

Details

PCM

PPM

PWM

ICM

Value

Author(s)

References

See Also

Examples

Create a motif.

Description

Usage

Arguments

Details

Value

Methods (by class)

Author(s)

See Also

Examples

Create random sequences.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Enrich for input motifs in a set of sequences.

Description

Usage

Arguments

Arabidopsis motif in `universalmotif` format.

Arabidopsis promoters as a `DNAStringSet`.

Example motif in `universalmotif` format.

Another example motif in `universalmotif` format.