dot-retrieve.peaks.as.granges: Converts the PEAKS BED12 format to a usable GRanges BED6...

In helen-zhu/DPDE4PM: A Method for Peak Merging Across Biological Replicates

Description

Converts the PEAKS BED12 format to a usable GRanges BED6 format for downstream analysis

Usage

.retrieve.peaks.as.granges(PEAKS, GENE, DF = F)

Arguments

PEAKS	A data frame containing the following columns, and potentially extras, usually found in a BED12 file, base 0 system
GENE	The ID of the gene
DF	Return as a data.frame. Otherwise, return as a GRanges object

Value

a data.frame or GRanges object in BED6 format containing only peaks assigned to a gene with an extra column for the peak index from where it was extracted and a sample id

helen-zhu/DPDE4PM documentation built on Feb. 17, 2021, 9:46 a.m.