runMethimputeGrid: Run Methimpute on binned genome

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

Run Methimpute on binned genome

Description

this function runs a HMM model on a genome binned using a sliding/non-sliding window approach

Usage

runMethimputeGrid(
  out.dir,
  fasta,
  win,
  step,
  genome,
  samplefiles,
  context,
  mincov,
  include.intermediate = FALSE,
  nCytosines
)

Arguments

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

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