RMotifScan {esATAC} | R Documentation

## Search Motif Position in Given Regions

### Description

Search motif position in genome according thr given motif and peak information.

### Usage

    atacMotifScan(
      atacProc,
      peak = NULL,
      genome = NULL,
      motifs = NULL,
      p.cutoff = 1e-06,
      scanO.dir = NULL,
      prefix = NULL,
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacMotifScan(
      atacProc,
      peak = NULL,
      genome = NULL,
      motifs = NULL,
      p.cutoff = 1e-06,
      scanO.dir = NULL,
      prefix = NULL,
      ...
    )

    motifscan(
      peak = NULL,
      genome = NULL,
      motifs = NULL,
      p.cutoff = 1e-06,
      scanO.dir = NULL,
      prefix = NULL,
      ...
    )

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacPeakCalling`.
`peak` | `Character` scalar. Input region path. UCSC bed file is recommented. Other file should be able to import as `GRanges` objects through `import`.
`genome` | BSgenome object, Default: from `getRefRc`.
`motifs` | either`PFMatrix`, `PFMatrixList`, `PWMatrix`, `PWMatrixList`.
`p.cutoff` | p-value cutoff for returning motifs.
`scanO.dir` | `Character` scalar. the output file directory. This function will use the name in motifs as the file name to save the motif position information in separate files.
`prefix` | prefix for Output file.
`...` | Additional arguments, currently unused.

### Details

This function scan motif position in a given genome regions.

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Wei Zhang

### See Also

`atacPeakCalling` `atacCutSiteCount`

### Examples

    ## Not run:
    library(R.utils)
    library(BSgenome.Hsapiens.UCSC.hg19)
    peak.path <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
    peak.path <- as.vector(bunzip2(filename = peak.path, destname = file.path(getwd(), "Example_peak1.bed"), ext="bz2", FUN=bzfile, overwrite=TRUE , remove = FALSE))

    motif <- readRDS(system.file("extdata", "MotifPFM.rds", package="esATAC"))

    motifscan(peak = peak.path, genome = BSgenome.Hsapiens.UCSC.hg19, motifs = motif)

    ## End(Not run)

[Package esATAC version 1.9.3 Index]