runMethimputeRegions: Run Methimpute for Regions

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

Run Methimpute for Regions

Description

This function runs a HMM model on identified Cytosine clusters

Usage

runMethimputeRegions(
  samplefiles,
  Regionfiles,
  genome,
  context,
  out.dir,
  include.intermediate = FALSE,
  mincov = 0,
  nCytosines = 0
)

Arguments

samplefiles	a text file containing path to samples and sample names, replicate info
Regionfiles	output of makeReg, containing coordinates of cytosine clusters/regions
genome	genome label for .e.g Arabidopsis
context	cytosine context
out.dir	output directory
include.intermediate	A logical specifying wheter or not the intermediate component should be included in the HMM.By default it is set as FALSE.
mincov	Minimum read coverage over cytosines
nCytosines	Minimum number of cytsoines

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