RMotifScanPair: Search Motif Position in Given Regions

RMotifScanPairR 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 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/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.