NEWS

universalmotif 1.24.2

BUG FIXES

Incorrect version number in last NEWS update.

universalmotif 1.24.1

BUG FIXES

Fixed another missed Rcpp bounds check warning.

universalmotif 1.22.3

BUG FIXES

Fixed make_DBscores() crash.

universalmotif 1.22.2

Added CITATION file.

universalmotif 1.22.1

BUG FIXES

Always check object sizes before indexing in universalmotif_cpp(). Fixes build timeouts on Bioconductor.

universalmotif 1.22.0

BUG FIXES

Address C++ compiler warnings.
Suppress warnings when using as.data.frame() on DataFrame objects in the SequenceSearches.Rmd vignette.

universalmotif 1.18.1

BUG FIXES

Fixed compilation flags causing errors on linux.

universalmotif 1.18.0

NEW FEATURES

read_meme(readsites.meta.tidy): New option to tidy the output of the readsites.meta option into a single data.frame.

MINOR CHANGES

create_motif(): More robust argument checking.
The rowMeans, colMeans, rowSums, and colSums generics are now imported from the MatrixGenerics package instead of BiocGenerics.

BUG FIXES

Clean up output of argument checks internal to exported functions.
Delete a reference in IntroductionToSequenceMotifs vignette to a non-exported function.
Delete outdated in MotifManipulation vignette regarding convert_motifs function.

universalmotif 1.16.0

NEW FEATURES

write_transfac(name.tag, altname.tag): New arguments to manually set the name and altname tags in the final TRANSFAC motifs.

MINOR CHANGES

write_matrix(positions): Partial argument matching allowed.
motif_tree(): Silence messages from ggtree.

BUG FIXES

create_motif(): Don't ignore the nsites argument when generating random motifs.
read_meme(): Correctly parse background if lines are prepended with a space.
convert_type(pseudocount): Change the pseudocount within the motif when performing a type conversion and the option is set.

universalmotif 1.14.1

BUG FIXES

read_meme(): Handle motif files with custom alphabets and no 'END' line in alphabet definition. Thanks to @manoloff (#24) for the bug report, and Spencer Nystrom for the fix (#25).

universalmotif 1.14.0

NEW FEATURES

enrich_motifs(mode, pseudocount): Choose whether to count motif hits once per sequence, and whether to add a pseudocount for P-value calculation.
New function, meme_alph(): Create MEME custom alphabet definition files.
merge_similar(return.clusters): Return the clusters without merging.
convert_motifs(): MotifDb-MotifList now available as an output format.

MINOR CHANGES

enrich_motifs(): RC argument now defaults to TRUE, increased max significance values, no.overlaps now defaults to TRUE. Additional columns showing the motif consensus sequence and percent of sequences with hits are now included.
scan_sequences(RC): Only print a warning if RC=TRUE for non-DNA/RNA motifs.
Reduced the size of the message when a pseudocount is added to motifs.

universalmotif 1.12.4

BUG FIXES

convert_motifs(): Properly handle TFBSTools class motifs with '*' as their strand. This was achieved by making the universalmotif object creator tolerant to using '*' as a user input. Thanks to David Oliver for the bug report (#22).

universalmotif 1.12.3

BUG FIXES

scan_sequences(): Previously this function did not account for the fact that duplicate sequence names are allowed within XStringSet objects. To better keep track of which sequence hits are associated with, an additional sequence.i column has been added which keeps track of the sequence number. This change also fixes a knock-on issue with enrich_motifs(), where sequences with duplicate names did not contribute to the count of sequences containing hits. Thanks to Alexandre Blais for mentioning this issue.

universalmotif 1.12.2

BUG FIXES

shuffle_sequences(..., method="markov"): Previously the returning sequences were longer by 1.

universalmotif 1.12.1

BUG FIXES

DNA ambiguity letters can be used with create_motif() when alphabet="DNA" is specified. Previously ambiguity letters only worked when alphabet was not specified.

universalmotif 1.12.0

NEW FEATURES

New function, sequence_complexity(): Using either the Wootton-Federhen, Trifonov, or DUST algorithms, calculate sequence complexity in sliding windows. A version for small arbitrary strings is also provided: calc_complexity().
New function, mask_ranges(): Similarly to mask_seqs(), mask specific positions in a XStringSet object by replacing the letters with a specific filler character.
New function, motif_range(): Get the min/max range of possible logodds scores for a motif.
New function, calc_windows(): Utility function for calculating coordinates for sliding windows.
New function, window_string(): Utility function for retrieving sliding windows in a string.
New function, slide_fun(): Utility function which wraps window_string() and vapply() together.
motif_pvalue(method): P-values and scores can now be calculated dynamically instead of exhaustively, substantially increasing both speed and accuracy for bigger jobs. The previous exhaustive method can still be used however, as the dynamic method does not allow non-finite values and thus must be pseudocount-adjusted.
scan_sequences(calc.pvals, calc.qvals, motif_pvalue.method, calc.qvals.method): The calc.pvals argument defaults to TRUE. The P-value calculation method now defaults to dynamic P-values (the previous method was an exhaustive calculation), though this can be changed via motif_pvalue.method. Additionally, adjusted P-values can be calculated as either BH, FDR or a Bonferroni-adjusted P-value. More details can be found in the Sequence Searches vignette.
write_homer(threshold, threshold.type): Finer control over the final motif logodds threshold included with the written motif is now available, using the style of argument parsing from scan_sequences(). The previous logodds_threshold argument is now deprecated and set to NULL, but if set (e.g. an older script is being re-run) then the old behaviour of write_homer() will be used.

MINOR CHANGES

New global option, options(pseudocount.warning): Disable the message printed when a motif is pseudocount-adjusted.
Slight performance gains in get_bkg() window code.
motif_pvalue(): Clarify that, indeed, background probabilities are taken into account when calculating P-values from score inputs. The background adjustment takes place during the initial conversion to PWM.
motif_pvalue(): When bkg.probs are provided, use those when converting to a PWM.
scan_sequences(): The default threshold is now 0.0001 (using threshold.type = "pvalue").
The axis text in view_motifs() is now black instead of grey.
create_motif(): When a named background vector is provided, it is sorted according to the alphabet characters.
scan_sequences(): Check that the sequences aren't shorter than the motifs.
print.universalmotif_df: Changed warning message when subsetting to an incomplete universalmotif_df object. Also added a way to turn off informative messages/warnings via the boolean universalmotif_df.warning global option.
Miscellaneous changes and additions to the vignettes and various function manual pages.

universalmotif 1.10.2

BUG FIXES

read_homer() now correct parses enrichment P-value and logodds score.

universalmotif 1.10.1

BUG FIXES

Restore temporarily disabled ggtree(layout="daylight") example in the MotifComparisonAndPvalues.Rmd vignette, as tidytree is now patched.
Fixed some awkwardness in view_motifs() panel spacing and title justification.

universalmotif 1.10.0

NEW FEATURES

A new data structure, universalmotif_df, has been made available. This allows for motifs to be manipulated as one would a data.frame object. The to_df() function is used to generate this stucture from lists of motifs. The update_motifs() function is used to apply changes to the actual motifs, and to_list() returns the actual motifs. Note that this is only meant as an option for more conveniently manipulating motif slots of multiple motifs simultaneously before returning them to a list; the universalmotif_df structure cannot be used in the various universalmotif functions. Additionally, requires_update() can be used to ascertain whether motifs are out of date in a universalmotif_df object. Many thanks to @snystrom for discussions and significant contributions.
view_motifs(): the universalmotif package now relies entirely on its own code to generate the polygon data used by ggplot2 to plot motifs, meaning the ggseqlogo import has been dropped. A number of new options are now available, including plotting multifreq logos and finer control over letter spacing. An effort has been made to ensure that the default behaviour of the function be unchanged from previous versions. This change should also allow for easier fixing of bugs and flexibility for future additions or changes.
New function, merge_similar(): identify and merge similar motifs in a list of motifs. Essentially, a wrapper around compare_motifs(), hclust(), cutree(), and merge_motifs().
New function, view_logo(): plot logos with matrix input instead of motif object input. Arbitrary column heights and multi-character letters are allowed.
New function, average_ic(): calculate the average information content for a list of motifs.
trim_motifs(..., trim.from): trim from both directions or just one.
shuffle_sequences(..., window, window.size, window.overlap): shuffle sequences iteratively in windows of specified size.
scan_sequences(..., return.granges): optionally return a GRanges object.
scan_sequences(..., no.overlaps, no.overlaps.by.strand, no.overlaps.strat): remove overlapping hits after scanning, preventing overlapping hits by the same motifs from being returned. This can optionally be done per strand. Either the first hit or the highest scoring hit can be preserved per set of overlapping hits. These new arguments can also be used in enrich_motifs().
scan_sequences(..., respect.strand): whether to scan the sequence strands according to the motif strand slot. Only applicable for DNA/RNA motifs. This option is also available in enrich_motifs().

MINOR CHANGES

Some additions and clean-up to documentation and vignettes.
Support for MotIV-pwm2 formatted motifs has been dropped, as the package is no longer a part of the current Bioconductor version.
read_matrix()/write_matrix(): the sep argument can now be NULL (no seperators.)
The Rdpack dependency has been dropped.
merge_motifs(): single-motif input now simply returns the motif instead of throwing an error.
view_motifs(..., dedup.names): now TRUE by default. Furthermore, the make.unique() function is now used to deduplicate names.
compare_motifs(..., method): the default comparison method has been changed back to PCC.

BUG FIXES

Using create_motif() with a single character no longer throws an error.
Generating random motifs with filled multifreq slots now works.

universalmotif 1.8.5

BUG FIXES

Found a typo in the consensus to PPM calculation for the DNA ambiguity letter Y which resulted in incorrect PPM values.

universalmotif 1.8.4

BUG FIXES

Fixed incorrect handling of the -alph parameter in run_meme() (reported by @Irenexzwen).

universalmotif 1.8.3

BUG FIXES

Fixed improper handling of MEME version string in read_meme().

universalmotif 1.8.2

BUG FIXES

Increase compliance with MEME motif format: motif files with missing alphabets/strand/bkg are now allowed and will be assumed to be DNA/+/uniform frequencies. A check for the MEME version is performed, though only a warning is given if not found.
Fixed typo in run_meme() missing dependency error message.

universalmotif 1.8.1

BUG FIXES

Fixed error when scan_sequences() is used with both RC = TRUE and calc.pvals = TRUE.
Fixed motif.i column in scan_sequences() results not reporting correctly when RC = TRUE.
Fixed memory access bug in motif_pvalue() when k was set to a value resulting in three or more submotifs.

universalmotif 1.8.0

NEW FEATURES

scan_sequences()/enrich_motifs() can now be used to scan/enrich for gapped motifs. A new section has been added to the SequenceSearches.Rmd vignette.
scan_sequences(..., use.gaps), enrich_motifs(..., use.gaps): ignore motif gap information.
read_meme(), write_meme(): now fully support custom alphabets.
prob_match(), prob_match_bkg(): calculate the probability of a motif match based on background frequencies of the motif object or provided values, respectively.
enrich_motifs(), get_matches(), get_scores(), motif_pvalue(), motif_score(), scan_sequences(), score_match(): new allow.nonfinite parameter, allowing for the functions to work even if non-finite values are present in the motif PWM.
read_matrix(..., comment): allows for comments to be ignored in motif files.
write_matrix(..., digits): control the number of digits to use for writing motif positions.
New mask_seqs() utility function: inject hard masks into sequences.
scan_sequences(..., warn.NA), enrich_motifs(..., warn.NA): new option which can disable warnings from non-standard letters being detected in the input sequences.
get_bkg(..., window, window.size, window.overlap): new options for calculating sequence background in windows.
get_bkg(..., merge.res): new option to return background information for individual sequences.
scan_sequences(..., calc.pvals): new option to calculate P-values for sequence hits. This is merely automating using the results from scan_sequences() to calculate P-values manually with motif_pvalue().
view_motifs(..., show.positions, show.positions.once, show.names): new options for customizing the look of plotted motifs.

MINOR CHANGES

read_matrix(..., positions): added partial argument matching.
create_sequences(), shuffle_sequences(), motif_pvalue(): the c++ random engine has been changed from std::default_random_engine to std::mt19937. This should allow for the same rng.seed value to result in the same output regardless of OS.
score_match() has been vectorized (alongside new prob_match() function).
The ape and ggtree packages are now no longer imported and must be installed seperately in order to use motif_tree().
The processx package is no longer imported and must be installed seperately in order to use run_meme().
The pseudocount slot is now shown when universalmotif class objects are printed.
get_bkg(): the list.out and as.prob options have been disabled. To simplify the function, the only possible output (exception: if to.meme is not NULL) is a DataFrame showing both counts and probabilities.
Changed the default look of motifs plotted by view_motifs().
General documentation cleanup.

BUG FIXES

Changing motif backgrounds with '[<-' will now make sure to set correct vector names.
get_bkg() will now correctly ignore non-standard letters and letters missing from the provided alphabet during counting.

universalmotif 1.6.4

BUG FIXES

cbind(): do not ignore the pseudocount slot.
Fixed typo in IntroductionToSequenceMotifs.Rmd.
Fixed U() function in IntroductionToSequenceMotifs.Rmd, no longer returns NA values if 0s are present.
read_cisbp(): no parsing errors for motifs with missing/partial header info.

universalmotif 1.6.3

BUG FIXES

scan_sequences(): commented out WIP code for scanning gapped motifs.

universalmotif 1.6.2

BUG FIXES

motif_tree(): 'daylight' layout is no longer disabled.

universalmotif 1.6.1

BUG FIXES

summarise_motif(): properly retrieves altname slot. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/9).
read_meme(): for LIKE type alphabets, make sure PROTEIN-LIKE is understood as being AA.

universalmotif 1.6.0

NEW FEATURES

log_string_pval(): small utility function to obtain the log of string-formatted p-values (such as those often carried in MEME-formatted motifs which are smaller than R's double.xmin limit). Likely only a temporary solution.
view_motifs(..., return.raw) option: instead of returning a plot type object, return the aligned motif matrices.
view_motifs(..., dedup.names) option: allows plotting of motifs with duplicated names by appending a unique string.
merge_motifs(..., new.name) option: assign a name to the new merged motif instead of collapsing the names of the merged motifs together.
round_motif() utility: round down very low letter-position scores to zero.

MINOR CHANGES

Removed most previously deprecated function arguments.
Make sure view_motifs(..., use.type = "ICM") properly sets ylim.
create_motif(): single motif positions can now be created.
create_motif(), character input: nsites slot is left empty is input is a single string. It is still filled if the input consists of multiple strings.
merge_motifs(): ALLR/ALLR_LL/KL/IS methods no longer add pseudocounts to the motifs. Instead, pseudocounts are added to temporary internal copies which are used for comparison and alignment. The original un-modified matrices are then combined.
read_meme(): now supports DNA-LIKE, RNA-LIKE, and AA-LIKE alphabets, though these will be treated as regular DNA, RNA, and AA alphabets, respectively. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/7).
Some cleanup to documentation and vignettes.
General code cleanup.

BUG FIXES

write_meme() now includes altname slot if filled. Contribution from Spencer Nystrom (https://github.com/bjmt/universalmotif/pull/5).
write_meme() checks for and removes any spaces/equal signs in motif names/altnames.
view_motifs(..., use.type = "ICM"): check for zero IC motifs, as these cannot be plotted by ggseqlogo.

universalmotif 1.4.10

BUG FIXES

Updated the warning from v1.4.9 to make users aware that the daylight layout will be permanently disabled for Bioconductor 3.10.

universalmotif 1.4.9

BUG FIXES

Temporarily disabling the 'daylight' layout for motif_tree() to get around a new bug.

universalmotif 1.4.8

BUG FIXES

Fixed buffer overflow error in motif_peaks().

universalmotif 1.4.7

BUG FIXES

Fixed dangling references in compare_motifs_helper.cpp and utils-exported.cpp.
Trying to subset a motif to a single column no longer throws an error.

universalmotif 1.4.6

BUG FIXES

scan_sequences(): will now actually emit a warning when non-standard letters are detected.

universalmotif 1.4.5

BUG FIXES

run_meme(): don't try and delete R's tempdir.

universalmotif 1.4.4

BUG FIXES

Minor fix to how args are fed to processx::run() in run_meme().

universalmotif 1.4.3

BUG FIXES

Suppress message output from library(TFBSTools) call in MotifManipulation.pdf vignette preamble code.

universalmotif 1.4.2

BUG FIXES

Stopped using BiocStyle, as a current bug was preventing the package from building successfully.

universalmotif 1.4.1

BUG FIXES

When using create_motif() with an AAStringSet object, amino acid letters will now be properly sorted and match the motif rows.

universalmotif 1.4.0

NEW FEATURES

scan_sequences(..., threshold.type) option: 'logodds.abs'. Allows the exact threshold scores to be provided.
compare_motifs() option: 'min.position.ic'. Prevent low-IC positions in an alignment from contributing to the final alignment score.
compare_motifs() option: 'score.strat'. Instruct the function how to deal with individual column scores in an alignment. This is also replaced the old way of choosing between sum and mean via prepending an 'M' to the metric name. Strategies for combining column scores include: sum, arithmetic mean, geometric mean, median, Fisher Z-transform, and weighted means.
Motif comparison metrics: average log-likelihood ratio, squared Euclidean distance, Hellinger distance, Bhattacharyya coefficient, Manhattan distance, lower limit average log-likelihood ratio, weighted Euclidean distance, weighted Pearson correlation coefficient.
compare_columns() utility: Compare two 1d numeric vectors using the comparison metrics from compare_motifs().
compare_motifs() option: 'output.report'. Generate an output report when 'compare.to' is provided, showing motif alignments of top matches.
get_scores() utility: Extract all possible scores from a motif.
filter_motifs(): Filter using the 'extrainfo' slot.
MotifComparisonAndPvalues.pdf vignette: the comparisons and P-values sections have been moved from AdvancedUsage.pdf to their own vignette. Higher order motifs, enrichment and run_meme() usage sections have been moved to SequenceSearches.pdf.

MINOR CHANGES

Removed 'random' shuffling method.
Using RcppThread instead of BiocParallel in several functions: compare_motifs(), create_sequences(), get_bkg(), motif_pvalue(), scan_sequences(), shuffle_sequences(). This means parallelization can occur within C++ code which is much faster than having to jump between R and C++. Currently motif_peaks(), read_motifs() and write_motifs() are the only remaining functions which offer optional BiocParallel usage.
Many performance improvements to functions relying on internal C++ code. Several internal R functions have been replaced with C++ versions.
Changed behaviour of make_DBscores() and motif comparison P-values. Re-calculated internal P-value databases.
For merge_motifs(..., use.type): now only accepts 'PPM'.
When comparing all motifs to all motifs with any method in compare_motifs(), the diagonal entries now properly show the max/min possible similarity/distance scores.
New internal merge_motifs() implementation. This also fixes a previous bug with incorrect PPM averaging.
read_homer(): the logodds score is converted to a P-value.
motif_pvalue(): New score calculator. Exact scores are still calculated the same (but with a faster C++ function), but approximate scores are now calculated by randomly generating score distributions from size 'k' motif score blocks.
motif_pvalue(): Added a safety check when trying to use this function with large motifs. Will throw a warning when nrow(matrix)^k > 1e8 and reduce k accordingly before continuing.
Adjusted P-value calculation in motif_peaks() to not display Pval = 0 so easily by instead estimating a normal distribution from random peaks.
convert_type(): make sure not to leave any zeros in bkg vector when a pseudocount greater than zero is used.
enrich_motifs(): split up 'hits' and 'positional' resuts into their own data.frames.
Replaced several instances of cat() with message() for printing progress updates.
Positional tests have been removed from enrich_motifs(). See motif_peaks() for testing motif-sequence positional preferences.
In read_meme(): E-values are now additionally stored in the extrainfo slot. This is to preserve E-values smaller than the R double precision limit.
In read_transfac(): Matrix values are rounded, to prevent errors when reading in matrices with non-integers.
Update JASPAR2018_CORE_DBSCORES with new compare_motifs() methods and params.
universalmotif print() method now returns the object invisibly, instead of NULL.

BUG FIXES

read_meme() will now properly parse background letter frequencies which span more than one line.
convert_motifs() will not error-out when trying to convert a PFMatrix with a family character vector longer than one.
Fixed P-value calculation when importing HOMER motifs. Peviously it would simply assume the log threshold value was the P-value. Now motif_pvalue() is used to properly calculate a P-value.

universalmotif 1.2.1

BUG FIXES

Mispelled variable in enrich_motifs().

universalmotif 1.2.0

NEW FEATURES

New motif_peaks() function: test for significantly overrepresented peaks of motif sites in a set of sequences.
New get_bkg() function: calculate background frequencies of sequence alphabets, including higher order backgrounds. Works for any sequence alphabet. Can also create MEME background format files.
read_meme() has a new option, readites.meta, which allows for reading individual motif site positions and P-values, as well as combined sequence P-values.
shuffle_sequences(..., method = "markov") works for any set of characters instead of just DNA/RNA.
shuffle_sequences(): new shuffling method, 'euler'. This allows for k>1 shuffling that preserves exact letter counts, as opposed to 'markov'. This method is set as the new default shuffling method.
create_sequences() has a new option "freqs" which allows for generating sequence from higher order backgrounds and any sequence alphabet (options "monofreqs", "difreqs" and "trifreqs" are now deprecated).
universalmotif objects can now hold onto higher order backgrounds.
motif_pvalue() with use.freq > 1 can calculate P-values from provided higher-order backgrounds, instead of assuming a uniform background.
add_multifreq() adds corresponding higher order background probabilities to motifs.
New get_klets() utility function: generate all possible k-lets for any set of characters.
New score_match() utility function: score a match for a particular motif.
New get_matches() utility function: get all possible motif matches above a certain score.
New count_klets() utility function: count all k-lets for any string of characters.
New motif_score() utility function: calculate motif score from input thresholds.
New shuffle_string() utility function: shuffle a string of character using one of three methods: euler, linear, and markov.
The native write_motifs()/read_motifs() universalmotif format is now YAML based. Motifs written before v1.2.0 can still be read by read_motifs().

MINOR CHANGES

Increased input security for character type parameters throughout.
Expanded motif_pvalue(), scan_sequences(), motif_tree() examples sections.
New vignette sections for motif_peaks() and get_bkg() added to SequenceSearches.Rmd.
Various vignette tweaks.
Fixed various spelling mistakes throughout, added Language field to Description, and added spell check to tests.
Documentation for the "random" shuffling method has been removed and a warning is shown when used to tell the user that it will be removed in the next minor update.
Generally increased test coverage.
The "k=1", "linear" and "markov" shuffling methods are much faster.
create_sequences() for higher order backgrounds is much faster.
Faster add_multifreqs(): slight improvement for DNA motifs, big improvement for non-DNA motifs.
sample_sites() has been rewritten for use.freq > 1: the probability of each letter in the site is now dependent on the previous letters (also faster and more memory efficient for any use.freq).
Improvement to calculating motif scores from p-value input: no longer guesses different scores, instead estimating a normal distribution of scores. This new approach is much, much faster and more memory efficient. It does however assume a uniform background.
The "score.pct" column in scan_sequences() results now represents the percent score based on the total possible score, not just the score between zero and the max possible score.
summarise_motifs() is much faster.
Objects in data/ are saved using serialization format version 3.
convert_motifs(motif, class = "universalmotif-universalmotif"): performs a validObject() check if "motif" is a universalmotif object.
The show() method for universalmotif objects performs a validObject() check first.
motif_rc() has a new option "ignore.alphabet", used to turn on or off the alphabet check (checks for DNA/RNA motif).
Added "overwrite" and "append" options to write_*() functions.
enrich_motifs(..., return.scan.results = FALSE): uses a slimmed down version of scan_sequences() which skips construction of the complete results data.frame, saving a tiny bit of time on large jobs.
compare_motifs() now includes log P-values. This way comparisons can still be properly ranked even if their P-values are below the machine limit.
convert_motifs() from MotifList (MotifDb) carries over dataSource.
If a MEME motif has two names, the second will be assigned as "altname" by read_meme().
Utilities documentation has been split into two: ?utils-motif and ?utils-sequence.

BUG FIXES

Fixed IC score calculation from character input in create_motif().
The internal DNA consensus letter calculation previously did not assign ambiguous letters when one PPM position was >0.5 and another was >0.25. This was unintended behaviour and will now output the proper ambigous DNA letter.

universalmotif 1.0.22

BUG FIXES

Fixed incorrect RcppExports code introduced in last patch.

universalmotif 1.0.21

BUG FIXES

Fixed an incorrect citation in motif_pvalue().

universalmotif 1.0.20

BUG FIXES

Fixed a bug introduced in previous patches where create_sequences() fails with alphabet = "RNA" and missing difreq/trifreq.

universalmotif 1.0.19

BUG FIXES

Fixed create_sequences(alphabet = "RNA") when providing difreq/trifreq.

universalmotif 1.0.18

BUG FIXES

Fixed alphabet letters being stripped from difreq and trifreq params in create_sequences().
Fixed an incorrect call to sample() when using create_sequences() with difreq.

universalmotif 1.0.17

BUG FIXES

Custom motif alphabets are properly sorted in the alphabet slot of motifs.
scan_sequences() properly matches custom sequence and motif alphabets.

universalmotif 1.0.16

BUG FIXES

scan_sequences() will now properly create a scoring matrix from motifs with pseudocounts of 0.

universalmotif 1.0.15

BUG FIXES

view_motifs() will now give an informative error message when trying to plot multiple motifs with non-unique names.

universalmotif 1.0.14

BUG FIXES

Fixed 'method' parameter documentation for motif_tree().

universalmotif 1.0.13

BUG FIXES

Fixed the error message given when a vector of incorrect length is used in a function.

universalmotif 1.0.12

BUG FIXES

motif_pvalue() no longer throws an error for motif_pvalue(..., pvalue = 0).
motif_tree() now works properly with dist objects as input.

universalmotif 1.0.11

BUG FIXES

The compare_motifs() example for min.mean.ic in the Advanced Usage vignette now makes more sense.

universalmotif 1.0.10

BUG FIXES

More strangely behaving MotifDb vignette code addressed in Advanced Usage vignette.

universalmotif 1.0.9

BUG FIXES

shuffle_motifs() now produces motifs of proper length.

universalmotif 1.0.8

BUG FIXES

Trying to prevent R CMD BUILD from changing the behaviour of vignette code involving MotifDb package.

universalmotif 1.0.7

BUG FIXES

merge_motifs() will not show repeat families/organisms in new merged motif.
show method will no longer show name slot instead of altname.

universalmotif 1.0.6

BUG FIXES

If MEME motif file has no strand info, assume 'strand = "+"', not 'strand = c("+", "-")'.

universalmotif 1.0.5

BUG FIXES

'read_meme()' can now read non-DNA/RNA motifs.
Removed duplicate line in run_meme.R.
'scan_sequences()' will not scan mismatching motif/sequence alphabets.
Verbose output from 'scan_sequences()' will now display correctly.
Using 'enrich_motifs()' and not finding any motif hits in the input sequences no longer throws an error.
Fixed threshold calculation in 'enrich_motifs()'.
'enrich_motifs()' will now show results for motifs which have hits in target sequences but none in bkg sequences.

universalmotif 1.0.4

BUG FIXES

Can now use 'view_motifs(..., tryRC=F)' without throwing an error.

universalmotif 1.0.3

BUG FIXES

Missed a couple [Biostrings::*StringSet-class] from last patch.
Updated README to reflect new installation method.
Wrapped instances of \link{} with \code{\link{}}.

universalmotif 1.0.2

BUG FIXES

'read_meme()' can now read meme result files with missing strand info.
Use \link{*StringSet} instead of [Biostrings::*StringSet-class] in documentation.
No longer load MotifDb package in examples on Windows.

universalmotif 1.0.1

BUG FIXES

TFBSTools motifs with multiple species can convert to universalmotif.
'scan_sequences()': will now ignore non-standard letters instead of crashing.

universalmotif 1.0.0

SIGNIFICANT USER-VISIBLE CHANGES

Changed the appearance of some of the vignette code blocks.
More documentation added in data.R.

BUG FIXES

Replaced for loop with 'lapply()' in add_multifreq.R L120-133.
Replaced for loop with 'lapply()' in enrich_motifs.R L327-330.
Replaced for loop with 'lapply()' in shuffle_motifs.R L77-80.
Using 'diag()' instead of for loop in 'fix_pcc_diag()' (compare_motifs.R).
Fixed 'read_motifs()' not parsing alphabet correctly.
Vignettes are now built using pdflatex instead of lualatex.

universalmotif 0.99.0

Ready for bioconductor.

universalmotif 0.98.0

Pre-bioconductor.