runjDMRgrid: Run jDMR on binned genome

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

Run jDMR on binned genome

Description

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

Usage

runjDMRgrid(
  out.dir,
  fasta.file,
  samplefiles,
  min.C,
  sliding.window = FALSE,
  genome,
  contexts = c("CG", "CHG", "CHH"),
  mincov = 0,
  include.intermediate = FALSE,
  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.
min.C	minimum number of cytosines in at least 90 percent of the bins/regions.
sliding.window	Logical specifying whether to use sliding windows while binning genome. By default non-sliding window with equal bin-size and step-size are used (set to FALSE).
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.
mincov	Minimum read coverage over cytosines. Default is set as 0.
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.
nCytosines	Minimum number of cytosines. Default is set as 0.

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