overlap_footprints_peaks: Overlap differential peaks and motif footprints

In jiang-junyao/IReNA: IReNA

Overlap differential peaks and motif footprints

Description

Because the running time of this function is too long, it's highly recommanded to use bedtools to implement this function

Usage

overlap_footprints_peaks(footprints, peak_bed)

Arguments

footprints	footprints file, generated by combine_footprints()
peak_bed	bed format of peak, first column should be 'chr', second column should be 'start', third column should be 'end'

Value

return data.frame contain footprints that overlap peaks

Examples

load(system.file("extdata", "test_peak.rda", package = "IReNA"))
load(system.file("extdata", "combined.rda", package = "IReNA"))
peak_bed <- get_bed(test_peak)
overlapped <- overlap_footprints_peaks(combined, peak_bed)

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.