calculate.mhl: calculate.mhl

In MPIIComputationalEpigenetics/WSHPackage: R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL

Description

This function computed the Methylation Haplotype Load (MHL) for all sites in a given annotation by employing the scripts downloaded from the paper's website

Usage

calculate.mhl(
  roi,
  bam.file,
  out.folder = getwd(),
  out.name = "mhl.txt",
  bam.type = "bismark"
)

Arguments

roi	Region of interest for which haplotype information should be computed
bam.file	path to bam file containing the reads
out.folder	folder to write the output
out.name	name of the output file
bam.type	alignment tools used to create the bam file

Value

a data frame containing the position in the reference genome and the MHL scores

MPIIComputationalEpigenetics/WSHPackage documentation built on Dec. 14, 2021, 11:49 a.m.