mergePlusMinusPeaks: Merge peaks from plus strand and minus strand

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Merge peaks from plus strand and minus strand

Description

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

Usage

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
)

Arguments

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.

Value

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

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. 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.

Examples

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

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.