annotateDMRs: Annotate DMRs

In jlab-code/jDMR: A heuristic DMR caller for large-scale WGBS data

Annotate DMRs

Description

This function takes gff3 files as input and outputs annotated DMRs in text and gff3 format. Additionally, a DMR count table is generated.

Usage

annotateDMRs(annotation, gff.files, gff3.out, input.dir, out.dir)

Arguments

annotation	annotation terms used to annotate DMRs
gff.files	multiple gff3 files can be supplied as a vector
gff3.out	a logical specifying whether output annotated files in gff3 format
input.dir	input directory containing filtered DMR matrix/matrices. Ideally any file containing 3 columns i.e (chr, start, stop) can be supplied.
out.dir	output directory

Value

output files containing annotated DMRs and DMR counts table.

jlab-code/jDMR documentation built on April 23, 2022, 11:02 a.m.