mergePlusMinusPeaks

0th

Percentile

Merge peaks from plus strand and minus strand

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

Keywords
misc
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

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

Aliases
  • mergePlusMinusPeaks
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")
}
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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