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(), ...)

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

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

### Arguments

`prevStep` | `Step-class` object scalar. It needs to be the return value of upstream process from `genBackground` or `enrichGenBackground` when it is not used in a pipeline. If it is used in a pipeline or `%>%` is applied on this function, any steps in this package is acceptable.
`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")`)
`...` | 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 1.0.0 Index]