MotifsInRegions: Find motifs in all input sequence regions

In wzthu/enrichTF: Transcription Factors Enrichment Analysis

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")

wzthu/enrichTF documentation built on March 30, 2020, 1:51 p.m.