mergePlusMinusPeaks {ChIPpeakAnno} | R Documentation

## Merge peaks from plus strand and minus strand

### 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")
    }

[Package ChIPpeakAnno version 3.12.7 Index]