runjDMRregions: Run jDMR for Regions

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

Run jDMR for Regions

Description

This function runs a HMM model on identified Cytosine clusters

Usage

runjDMRregions(
  out.dir,
  fasta.file,
  samplefiles,
  genome,
  contexts = c("CG", "CHG", "CHH"),
  include.intermediate = FALSE,
  mincov = 0,
  nCytosines = 0
)

Arguments

out.dir	output directory
fasta.file	path to genome fasta file
samplefiles	a text file containing path to samples and sample names. For control/treatment data an additional column specifying the replicates is required.
genome	Genome name as a string .e.g Arabidopsis or Human etc
contexts	cytosine contexts as a vector. By default this option is set for all 3 cytosine contexts CG, CHG and CHH.
include.intermediate	A logical specifying whether or not the intermediate component should be included in the HMM model.By default it is set as FALSE.
mincov	Minimum read coverage over cytosines. Default is set as 0.
nCytosines	Minimum number of cytosines. Default is set as 0.

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