VennPeaks reads in data.tables from ReadPeaks to produce an output suitable for visualization via a Venn diagram.

VennPeaks(peaks.list, plot = TRUE, weighted = FALSE,
  return.overlaps.all = FALSE, return.overlaps.matrix = FALSE)

Arguments

return.overlaps.all

Returns the overlaps matrix for each sample:peakid to extract sets

return.overlaps.matrix

Returns summary matrix used to create venn diagram

peaks

Up to three sets of peaks as data.frame that can be converted to GRanges

peaks.anno

Cognate annotation via annotatePeaks.pl of output from findPeaks.

Value

data.table combining peak and annotation info.

Examples

TF.ReadPeaks <- ReadPeaks(TF.peaks, TF.anno)
TF2.ReadPeaks <- ReadPeaks(TF2.peaks, TF2.anno)
VennPeaks(list(TF.ReadPeaks, TF2.ReadPeaks))