getCommPeaks: Do overlap over input peaks files in same condition, then...

In yancychy/DiffChIPL: ChIP-seq differential analysis (DiffChIPL)

Do overlap over input peaks files in same condition, then merge the control and treatment peaks

Description

Do overlap over input peaks files in same condition, then merge the control and treatment peaks

Usage

getCommPeaks(inputF, controlName = "", treatmentName = "", peakLen = 2)

Arguments

inputF	file path, the file format is same to DiffBind input file to show the sample name, TF, Control, Treatment, bam file path, and peak files path.
controlName	string The control name
treatmentName	string The treatment name
peakLen	integer The length of peak threshold (>2)

Value

list pr GRanges objects, common peak coordinates between two conditions peakL list of GRanges objects, which contains the peak coordinate in each peak file

Examples

peaksAll = getCommPeaks(inputF, controlName="", treatmentName="",)

yancychy/DiffChIPL documentation built on Dec. 24, 2024, 11:26 p.m.