mergePlusMinusPeaks {ChIPpeakAnno} | R Documentation |
Merge peaks from plus strand and minus strand within certain distance apart, and output merged peaks as bed format.
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 )
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 |
output the merged peaks in bed file and a data frame of the 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
annotatePeakInBatch, findOverlappingPeaks, makeVennDiagram
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") }