RPeakComp {esATAC} | R Documentation

## 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`.
`bedInput2` | `Character` scalar. Input peak file path. UCSC bed file is recommented. Other file should be able to import as `GRanges` objects through `import`.
`bedOutput` | The output file path. File name order: bedInput1 specific peaks, bedInput2 specific peaks, 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)

[Package esATAC version 1.4.5 Index]