filterRegions: Pre-filtering of candidate DMRs.

In haowulab/TRESS: Toolbox for mRNA epigenetics sequencing analysis

Pre-filtering of candidate DMRs.

Description

This function filters out candidate DMRs who have small (e.g., less than 25% quantile) marginal coefficient of variation (CV) in methylation ratio.

Usage

filterRegions(Candidates, quant = 0.25)

Arguments

Candidates	A list containing "Counts", "Regions", "sf" for read counts, genomic coordinate of each candidate DMR and size factor of all samples. See output of CallCandidates.
quant	A percentage to specify a quantile cutoff. Regions with CV smaller than this quantile would be filtered out. Default is 25%.

Value

A list with the same structure with input "Candidates" but with a smaller number of candidate DMRs.

Examples

# A toy example
data(DMR_M3vsWT) # data from TRESS
sub.DMR_M3vsWT = filterRegions(DMR_M3vsWT)

haowulab/TRESS documentation built on Aug. 27, 2022, 7:11 p.m.