MotifsInRegions {enrichTF}R Documentation

Find motifs in all input sequence regions

Description

Scan for motif occurrences using the prepared PWMs and obtain the promising candidate motifs in these regions.

Usage

enrichFindMotifsInRegions(prevStep, inputRegionBed = NULL,
  outputRegionMotifBed = NULL, motifRc = c("integrate", "jaspar",
  "pwmfile"), inputPwmFile = getRefFiles("motifpwm"),
  genome = getGenome(), threads = getThreads(), ...)

## S4 method for signature 'Step'
enrichFindMotifsInRegions(prevStep,
  inputRegionBed = NULL, outputRegionMotifBed = NULL,
  motifRc = c("integrate", "jaspar", "pwmfile"),
  inputPwmFile = getRefFiles("motifpwm"), genome = getGenome(),
  threads = getThreads(), ...)

findMotifsInRegions(inputRegionBed, outputRegionMotifBed = NULL,
  motifRc = c("integrate", "jaspar", "pwmfile"),
  inputPwmFile = getRefFiles("motifpwm"), genome = getGenome(),
  threads = getThreads(), ...)

Arguments

prevStep

Step-class object scalar. This parameter is available when the upstream step function (printMap() to see the previous functions) have been sucessfully called. Accepted value can be the object return by any step function or be feed by %>% from last step function.

inputRegionBed

Character scalar. BED file for regions including foreground and background sequences.

outputRegionMotifBed

Character scalar. BED file for regions with motif candidates. Default: NULL (generated base on inputForegroundBed)

motifRc

Character scalar. Motif Resources can be one of "integrate" (integrated by us and can be download from internet automatically if call the function setGenome("hg19")), "jaspar" package JASPAR2018, or "pwmfile" (User defined PWM file. inputPwmFile is required).

inputPwmFile

Character scalar. when "pwmfile" is set for motifRc, use this argument to provide PWM file directory.

genome

Character scalar. Bioconductor supported genome, such as "hg19", "mm10", etc. Default: NULL (e.g. after library (enrichTF), you can call function setGenome("hg19"))

threads

Integer scalar. The maximum threads that will be used in this step. Default: getThreads()

...

Additional arguments, currently unused.

Details

Scan for motif occurrences using the prepared PWMs and obtain the promising candidate motifs in these regions.

Value

An invisible EnrichStep-class object (Step-class based) scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

genBackground findMotifsInRegions tfsEnrichInRegions

Examples

setGenome("testgenome") #Use "hg19","hg38",etc. for your application
foregroundBedPath <- system.file(package = "enrichTF",
    "extdata","testregion.bed")
gen <- genBackground(inputForegroundBed = foregroundBedPath)
findMotif <- enrichFindMotifsInRegions(gen,motifRc="integrate")
[Package enrichTF version 1.2.3 Index]