RPeakComp: Find the overlap or differential peaks between two samples.

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

Find the overlap or differential peaks between two samples.

Description

This function compares two peak file and report overlap or differential peaks according to the parameter "operation".

Usage

atacPeakComp(
  atacProcPeak1,
  atacProcPeak2,
  bedInput1 = NULL,
  bedInput2 = NULL,
  bedOutput = NULL,
  olap.rate = 0.2,
  ...
)

## S4 method for signature 'ATACProc'
atacPeakComp(
  atacProcPeak1,
  atacProcPeak2,
  bedInput1 = NULL,
  bedInput2 = NULL,
  bedOutput = NULL,
  olap.rate = 0.2,
  ...
)

peakcomp(
  bedInput1 = NULL,
  bedInput2 = NULL,
  bedOutput = NULL,
  olap.rate = 0.2,
  ...
)

Arguments

atacProcPeak1	ATACProc-class object scalar. It has to be the return value of upstream process: atacPeakCalling.
atacProcPeak2	ATACProc-class object scalar. It has to be the return value of upstream process: atacPeakCalling.
bedInput1	Character scalar. Input peak file path. UCSC bed file is recommented. Other file should be able to import as GRanges objects through import in package rtracklayer.
bedInput2	Character scalar. Input peak file path. UCSC bed file is recommented. Other file should be able to import as GRanges objects through import in package rtracklayer.
bedOutput	The output file path for overlap peaks.
olap.rate	Overlap rate, if the overlap region between 2 peak is more than this rate of the short peak, these two peak are considered to be overlap and will be merged to a bigger peak. Default: 0.2. NOTICE: multi-peak will be merged together!
...	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Wei Zhang

See Also

atacPeakCalling

Examples

library(R.utils)
p1bz <- system.file("extdata", "Example_peak1.bed.bz2", package="esATAC")
p2bz <- system.file("extdata", "Example_peak2.bed.bz2", package="esATAC")
## Not run: 
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))
output <- peakcomp(bedInput1 = peak1_path, bedInput2 = peak2_path,
olap.rate = 0.1)

## End(Not run)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.