RMotifScanPair {esATAC} | R Documentation

## Search Motif Position in Given Regions

### Description

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

### Usage

    atacMotifScanPair(atacProc, peak1 = NULL, peak2 = NULL, background = NULL,
      genome = NULL, motifs = NULL, p.cutoff = 1e-04, scanO.dir = NULL,
      prefix = NULL, ...)

    ## S4 method for signature 'ATACProc'
    atacMotifScanPair(atacProc, peak1 = NULL, peak2 = NULL,
      background = NULL, genome = NULL, motifs = NULL, p.cutoff = 1e-04,
      scanO.dir = NULL, prefix = NULL, ...)

    motifscanpair(peak1 = NULL, peak2 = NULL, background = NULL,
      genome = NULL, motifs = NULL, p.cutoff = 1e-04, scanO.dir = NULL,
      prefix = NULL, ...)

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacpeakComp`.
`peak1` | peak file path.
`peak2` | peak file path.
`background` | background peak file path.
`genome` | BSgenome object, Default: from `setConfigure`.
`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. Order: peak1, peak2, backgroud.
`...` | 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

`atacpeakComp`

### Examples

    library(R.utils)
    library(BSgenome.Hsapiens.UCSC.hg19)
    p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
    p2bz <- system.file("extdata", "Example_peak2.bed.bz2", package="esATAC")
    peak1_path <- as.vector(bunzip2(filename = p1bz,
    destname = file.path(getwd(), "Example_peak1.bed"),
    ext="bz2", FUN=bzfile, overwrite=TRUE , remove = FALSE))
    peak2_path <- as.vector(bunzip2(filename = p2bz,
    destname = file.path(getwd(), "Example_peak2.bed"),
    ext="bz2", FUN=bzfile, overwrite=TRUE, remove = FALSE))
    peakcom.output <- peakcomp(bedInput1 = peak1_path, bedInput2 = peak2_path,
    olap.rate = 0.1)

    motif <- readRDS(system.file("extdata", "MotifPFM.rds", package="esATAC"))
    output <- atacMotifScanPair(atacProc = peakcom.output,
    genome = BSgenome.Hsapiens.UCSC.hg19, motifs = motif)

[Package esATAC version 1.8.0 Index]