makeDMRmatrix: Builds a DMR matrix for all samples
In jlab-code/jDMR: A heuristic DMR caller for large-scale WGBS data

makeDMRmatrix

R Documentation

Builds a DMR matrix for all samples

This function generates a binary matrix, a matrix of recalibrated methylation levels and posterior probabilities for all samples.

makeDMRmatrix(
  context = c("CG", "CHG", "CHH"),
  samplefiles,
  input.dir,
  out.dir,
  include.intermediate = FALSE
)

`context`	cytosine context
`samplefiles`	file containing full path of base level methylation calls, sample names and replicates(optional)
`input.dir`	input directory containing all region level methylome calls
`out.dir`	output directory
`include.intermediate`	A logical specifying whether or not the intermediate component should be included in the HMM model.By default this option is set as FALSE.