RMotifScanPair: Search Motif Position in Given Regions

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

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 getRefRc.
motifs	eitherPFMatrix, 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

## Not run: 
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)

## End(Not run)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.