mergePlusMinusPeaks: Merge peaks from plus strand and minus strand

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Merge peaks from plus strand and minus strand within certain distance apart, and output merged peaks as bed format.

Usage

mergePlusMinusPeaks(
  peaks.file,
  columns = c("name", "chromosome", "start", "end", "strand", "count", "count",
    "count", "count"),
  sep = "\t",
  header = TRUE,
  distance.threshold = 100,
  plus.strand.start.gt.minus.strand.end = TRUE,
  output.bedfile
)

Arguments

peaks.file	Specify the peak file. The peak file should contain peaks from both plus and minus strand
columns	Specify the column names in the peak file
sep	Specify column delimiter, default tab-delimited
header	Specify whether the file has a header row, default TRUE
distance.threshold	Specify the maximum gap allowed between the plus stranded and the nagative stranded peak
plus.strand.start.gt.minus.strand.end	Specify whether plus strand peak start greater than the paired negative strand peak end. Default to TRUE
output.bedfile	Specify the bed output file name

Value

output the merged peaks in bed file and a data frame of the bed format

Author(s)

Lihua Julie Zhu

References

Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237

See Also

annotatePeakInBatch, findOverlappingPeaks, makeVennDiagram

Examples

if (interactive())
{
    data(myPeakList)
    data(TSS.human.NCBI36)
    library(matrixStats)
        peaks <- system.file("extdata", "guide-seq-peaks.txt", 
                              package = "ChIPpeakAnno")
        merged.bed <- mergePlusMinusPeaks(peaks.file = peaks, 
                                          columns=c("name", "chromosome", 
                                                    "start", "end", "strand", 
                                                    "count", "count"), 
                                          sep = "\t", header = TRUE,  
                                          distance.threshold = 100,  
                                plus.strand.start.gt.minus.strand.end = TRUE, 
                                          output.bedfile = "T2test100bp.bed")
}

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.