filterDMRmatrix: filter DMR matrix

In rashmihazarika/jDMR: A heuristic DMR caller for population-level WGBS data

filter DMR matrix

Description

Filters non-polymorphic patterns by default.

Usage

filterDMRmatrix(
  epiMAF.cutoff = NULL,
  replicate.consensus = NULL,
  gridDMR,
  data.dir
)

Arguments

epiMAF.cutoff	Filter for Minor Epi-Allele frequency. By default this option is set to NULL. Applicable for population level data.
replicate.consensus	Percentage of concordance in methylation states among samples with multiple replicates. By default this option is set to NULL. Useful for Control/treatment data
gridDMR	Logical specifying if grid DMR approach was used for calling DMRs.
data.dir	Directory containing DMR matrix files. Looks for files with suffix, _StateCalls.txt and _rcMethlvl.txt

rashmihazarika/jDMR documentation built on Jan. 30, 2024, 8:46 a.m.