Package 'scanMiRApp'

enrichedMirTxPairs

Description

Identifies pairs of miRNA and target transcripts that have an unexpectedly high number of sites.

Usage

enrichedMirTxPairs(m, minSites = 5, max.binom.p = 0.001)

Arguments

m	A GRanges of matches, as produced by findSeedMatches. This will be filtered down to only 8mer and 7mer sites.
minSites	The minimum number of sites for a given miRNA-target pair to be considered.
max.binom.p	The maximum binomial p-value of miRNA-target pairs.

Value

A data.frame of top combinations, including number of sites and the log-transformed binomial p-value.

Examples

# we create a dummy scan (see `runFullScan`)
library(scanMiR)
seqs <- getRandomSeq(n=10)
mirs <- c("TTGTATAA","AGCATTAA")
m <- findSeedMatches(seqs,mirs,verbose=FALSE)
# we look for enriched pairs
res <- enrichedMirTxPairs(m, minSites=1, max.binom.p=1)
res

---

Example 'fake' TxDb object

Description

A fake transcript database used for examples.

Value

a named character vector of length 1.

---

getTranscriptSequence

Description

Utility wrapper to extracts the sequence of a given transcript (UTR or CDS+UTR).

Usage

getTranscriptSequence(
  tx = NULL,
  annotation,
  annoFilter = NULL,
  extract = c("UTRonly", "withORF", "exons"),
  ...
)

Arguments

tx	The ensembl ID of the transcript(s)
annotation	A ScanMiRAnno object.
annoFilter	An optional 'AnnotationFilter' or 'AnnotationFilterList' to further filter the set of transcripts to be extracted
extract	Which parts of the transcripts to extract. For 'UTRonly' (default) only the 3' UTR regions are extracted, 'withORF' additionally extracts the coding regions, and 'exons' extracts all exons
...	Passed to AnnotationHub

Value

A DNAStringSet.

Examples

anno <- ScanMiRAnno("fake")
seq <- getTranscriptSequence( tx="ENSTFAKE0000056456", annotation=anno )

---

IndexedFst

Description

Objects of the IndexedFst class enable fast named random access to FST files. This is particularly appropriate for large data.frames which often need to be accessed according to the (e.g. factor) value of a particular column.

Usage

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

## S4 method for signature 'IndexedFst'
summary(object)

## S4 method for signature 'IndexedFst'
names(x)

## S4 method for signature 'IndexedFst'
length(x)

## S4 method for signature 'IndexedFst'
lengths(x)

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

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

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

## S4 method for signature 'IndexedFst,ANY,ANY'
x[[i, j = NULL, ...]]

## S4 method for signature 'IndexedFst,ANY,ANY,ANY'
x[i, j = NULL, ..., drop = TRUE]

## S4 method for signature 'IndexedFst'
x$name

## S4 method for signature 'IndexedFst'
head(x, n = 6L, ...)

## S4 method for signature 'IndexedFst'
as.data.frame(x, name)

Arguments

object	an IndexedFst object
x	an IndexedFst object
i	the desired index (either numeric or name)
j, drop	ignored
...	ignored
name	the indexed name to fetch
n	the desired number of rows

Value

Depends on the method

Author(s)

Pierre-Luc Germain, [email protected]

See Also

saveIndexedFst, loadIndexedFst

Examples

# we first create and save an indexed FST file
tmp <- tempdir()
f <- system.file(tmp, "test")
d <- data.frame( category=sample(LETTERS[1:4], 10000, replace=TRUE),
                 var2=sample(LETTERS, 10000, replace=TRUE),
                 var3=runif(10000) )
format(object.size(d),units="Kb")
saveIndexedFst(d, "category", f)
rm(d)
# we then load the index, and can use category names for random access:
d <- loadIndexedFst(f)
format(object.size(d),units="Kb")
nrow(d)
names(d)
head(d$A)

---

Saving and loading IndexedFst

Description

Functions to save or load and indexed fst file

Saves a data.frame (or GRanges object) into an indexed FST file.

Usage

loadIndexedFst(file, nthreads = 1)

saveIndexedFst(
  d,
  index.by,
  file.prefix,
  nthreads = 1,
  index.properties = NULL,
  add.info = list(),
  ...
)

Arguments

file	Path to the fst file, it's index (.idx), or their prefix.
nthreads	Number of threads to use for reading (default 1). This does not affect the loading of the index itself, but will affect all downstream reading operations performed on the object. If NULL, will use 'fst::threads_fst()'.
d	A data.frame or GRanges object
index.by	A column of 'd' by which it should be indexed.
file.prefix	Path and prefix of the output files.
index.properties	An optional data.frame of properties, with the levels of 'index.by' as row names.
add.info	An optional list of additional information to save.
...	Passed to 'write.fst'

Value

'loadIndexedFst' returns an object of class IndexedFst-class, and 'saveIndexedFst' returns nothing.

See Also

IndexedFst-class

IndexedFst-class

Examples

# we first create and save an indexed FST file
tmp <- tempdir()
f <- system.file(tmp, "test")
d <- data.frame( category=sample(LETTERS[1:4], 10000, replace=TRUE),
                 var2=sample(LETTERS, 10000, replace=TRUE),
                 var3=runif(10000) )
saveIndexedFst(d, "category", f)
# we then load the index, and can use category names for random access:
d <- loadIndexedFst(f)

---

plotSitesOnUTR

Description

Wrapper function with minimal arguments to plot scanMiR-Binding sites on 3'UTRs of specified transcripts. The red dashed line indicates the background threshhold is indicated, the lightblue dashed line shows the average 8mer dissociation rate of the given miRNA

Usage

plotSitesOnUTR(
  tx,
  annotation,
  miRNA = NULL,
  label_6mers = FALSE,
  label_notes = FALSE,
  verbose = TRUE,
  ...
)

Arguments

tx	An ensembl TranscriptID
annotation	A ScanMiRAnno object.
miRNA	A miRNA name in the mirbase format (eg. "hsa-miR-485-5p"), a 'KdModel', or a miRNA sequence or target seed.
label_6mers	Logical whether to label 6mer sites in the plot
label_notes	Logical whether to label special sites in the plot (as TDMD or Slicing)
verbose	Logical; whether to print updates on the processing
...	Any further arguments passed to findSeedMatches

Value

Returns a ggplot.

Examples

anno <- ScanMiRAnno("fake")
plotSitesOnUTR( tx="ENSTFAKE0000056456", annotation=anno,
                miRNA="hsa-miR-155-5p" )

---

runFullScan

Description

Runs a full miRNA scan on all protein-coding transcripts (or UTRs) of an annotation.

Usage

runFullScan(
  annotation,
  mods = NULL,
  annoFilter = NULL,
  extract = c("UTRonly", "withORF", "exons"),
  onlyCanonical = TRUE,
  shadow = 15,
  cores = 1,
  maxLogKd = c(-1, -1.5),
  save.path = NULL,
  ...
)

Arguments

annotation	A ScanMiRAnno object
mods	An optional 'KdModelList' (defaults to the one in 'annotation')
annoFilter	An optional 'AnnotationFilter' or 'AnnotationFilterList' to filter the set of transcripts to be extracted
extract	Which parts of the transcripts to extract. For 'UTRonly' (default) only the 3' UTR regions are extracted, 'withORF' additionally extracts the coding regions, and 'exons' extracts all exons
onlyCanonical	passed to findSeedMatches
shadow	The size of the ribosomal shadow at the UTR starts
cores	The number of threads to use. Alternatively accepts a BiocParallelParam-class, as for instance produced by MulticoreParam.
maxLogKd	The maximum log_kd of sites to report
save.path	Optional, the path to which to save the results
...	Arguments passed to findSeedMatches

Value

A 'GRanges' object

Examples

anno <- ScanMiRAnno("fake")
m <- runFullScan( annotation=anno )
m

---

ScanMiRAnno

Description

ScanMiRAnno

Usage

ScanMiRAnno(
  species = NULL,
  genome = NULL,
  ensdb = NULL,
  models = NULL,
  scan = NULL,
  aggregated = NULL,
  version = NULL,
  addDBs = list(),
  ...
)

Arguments

species	The species/build acronym for automatic construction; if omitted, 'genome' and 'ensdb' should be given. Current possible values are: GRCh38, GRCm38, GRCm39, Rnor_6.
genome	A BSgenome-class, or a TwoBitFile
ensdb	An EnsDb-class (or a TxDb-class) object
models	An optional KdModelList
scan	An optional full scan (IndexedFst or GRanges)
aggregated	An optional per-transcript aggregation (IndexedFst or data.frame)
version	optional ensembl version
addDBs	A named list of additional tx-miRNA databases, each of which should be a data.frame with the columns 'transcript', 'miRNA', and 'score'.
...	Arguments passed to 'AnnotationHub'

Value

A 'ScanMiRAnno' object

Examples

anno <- ScanMiRAnno(species="fake")
anno

---

Methods for the ScanMiRAnno class

Description

Methods for the ScanMiRAnno class

Usage

## S4 method for signature 'ScanMiRAnno'
summary(object)

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

Arguments

object

An object of class ScanMiRAnno

Value

Depends on the method.

See Also

ScanMiRAnno

---

scanMiRApp A wrapper for launching the scanMiRApp shiny app

Description

scanMiRApp A wrapper for launching the scanMiRApp shiny app

Usage

scanMiRApp(annotations = NULL, ...)

Arguments

annotations	A named list of ScanMiRAnno objects. If omitted, will use the base ones.
...	Passed to scanMiRserver

Value

A shiny app

Examples

if(interactive()){
  anno <- ScanMiRAnno("fake")
  scanMiRApp(list(fakeAnno=anno))
}

---

scanMiRserver

Description

Server function for the scanMiR shiny app. Most users are expected to use scanMiRApp instead.

Usage

scanMiRserver(
  annotations = list(),
  modlists = NULL,
  maxCacheSize = 10 * 10^6,
  BP = SerialParam()
)

Arguments

annotations	A named list of ScanMiRAnno object.
modlists	A named list of 'KdModelList' objects. If omitted, will fetch it from the annotation objects.
maxCacheSize	Maximum cache size in bytes.
BP	BPPARAM for multithreading

Value

A shiny server function

Examples

# we'd normally fetch a real annotation:
# anno <- ScanMiRAnno("Rnor_6")
# here we'll use a fake one:
anno <- ScanMiRAnno("fake")
srv <- scanMiRserver(list(fake=anno))

---

scanMiRui

Description

UI for the scanMiR app.

Usage

scanMiRui()

Value

A shiny ui

Examples

ui <- scanMiRui()

---