assign_peak_segments {chipenrich} | R Documentation |
Determine all overlaps between the set of input regions peaks
and the given locus definition locusdef
. In addition, report where each overlap begins and ends, as well as the length of the overlap.
assign_peak_segments(peaks, locusdef)
peaks |
A |
locusdef |
A locus definition object from |
Typically, this function will not be used alone, but inside chipenrich()
with method = 'broadenrich'
.
A data.frame
with columns for peak_id, chr, peak_start, peak_end, gene_locus_start, gene_locus_end, gene_id, overlap_start, overlap_end, peak_overlap
. The result is used in num_peaks_per_gene()
.
data('locusdef.hg19.nearest_tss', package = 'chipenrich.data') data('tss.hg19', package = 'chipenrich.data') file = system.file('extdata', 'test_assign.bed', package = 'chipenrich') peaks = read_bed(file) assigned_peaks = assign_peak_segments( peaks = peaks, locusdef = locusdef.hg19.nearest_tss)