filterDMRmatrix: filter DMR matrix

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

filter DMR matrix

Description

Filters non-polymorphic patterns by default.

Usage

filterDMRmatrix(
  epiMAF.cutoff = NULL,
  replicate.consensus = NULL,
  gridDMR = TRUE,
  data.dir,
  rc.methlvl.out = FALSE,
  context.specific.DMRs = TRUE
)

Arguments

epiMAF.cutoff	Filter for Minor Epi-Allele frequency (for e.g 0.33). Applicable for population level data. By default this option is set to NULL.
replicate.consensus	Percentage of concordance in methylation states among samples with multiple replicates. Applicable for Control/treatment data. By default this option is set to NULL.
gridDMR	Logical specifying if grid DMR approach was used for calling DMRs. By default this option is set to TRUE. If Cluster approach was used, set it to FALSE.
data.dir	Directory containing DMR matrix files. Looks for files with suffix("_StateCalls.txt" and "_rcMethlvl.txt")
rc.methlvl.out	Logical whether to output filtered matrix with methylation levels. By default this option is set to FALSE.
context.specific.DMRs	Logical whether to output list of CG-only, CHG-only, CHH-only, nonCG and multi-context DMRs. By default this option is set to TRUE.

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