peaksToGRanges: List of peaks to GRanges

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

List of peaks to GRanges

Description

Wrapper function for makeGrangesFromDataFrame() from the GenomicRanges package to build GRanges objects from character list of chromosomal regions because this is a common format to receive peak information.

Usage

peaksToGRanges(region_list, sep)

Arguments

region_list	character list or vector of chromosomal regions/peaks in form chromosomenumber(sep)start(sep)end eg. Chr1-345678-398744
sep	separator between information pieces of string (conventionally "-" or ".")

Value

GRanges corrsponding to input list of region information

Note

If region_list is a dataframe you should use the GenomicRanges function makeGRangesFromDataFrame which this function applies

Examples

data(schepPeaks)

schepGranges = peaksToGRanges(schepPeaks, sep = "-")

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.