mergePlusMinusPeaks: Merge peaks from plus strand and minus strand
In GUIDEseq: GUIDE-seq analysis pipeline

Description Usage Arguments Value Author(s) References Examples

Merge peaks from plus strand and minus strand with required orientation and within certain distance apart

mergePlusMinusPeaks(peaks.gr, peak.height.mcol = "count", 
    bg.height.mcol = "bg", distance.threshold = 40L, 
    max.overlap.plusSig.minusSig = 30L,
    plus.strand.start.gt.minus.strand.end = TRUE, output.bedfile)

`peaks.gr`	Specify the peaks as GRanges object, which should contain peaks from both plus and minus strand. In addition, it should contain peak height metadata column to store peak height and optionally background height.
`peak.height.mcol`	Specify the metadata column containing the peak height, default to count
`bg.height.mcol`	Specify the metadata column containing the background height, default to bg
`distance.threshold`	Specify the maximum gap allowed between the plus stranded and the negative stranded peak, default 40. Suggest set it to twice of window.size used for peak calling.
`max.overlap.plusSig.minusSig`	Specify the cushion distance to allow sequence error and inprecise integration Default to 30 to allow at most 10 (30-window.size 20) bp (half window) of minus-strand peaks on the right side of plus-strand peaks. Only applicable if plus.strand.start.gt.minus.strand.end is set to TRUE.
`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, which is used for off target analysis subsequently.

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

`mergedPeaks.gr`	merged peaks as GRanges
`mergedPeaks.bed`	merged peaks in bed format

Lihua Julie Zhu

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. Zhu L.J. (2013) Integrative analysis of ChIP-chip and ChIP-seq dataset. Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8\_8.

if (interactive())
{
    data(peaks.gr)
    mergedPeaks <- mergePlusMinusPeaks(peaks.gr = peaks.gr,
        output.bedfile = "mergedPeaks.bed")
    mergedPeaks$mergedPeaks.gr
    head(mergedPeaks$mergedPeaks.bed)
}