calculate.qfdrp: calculate.qfdrp

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 calculates the qFDRP scores for the reads given in the bam files for the CpGs present in the annotation.

Usage

calculate.qfdrp(
  bam.file,
  anno,
  log.path = getwd(),
  cores = 1,
  window.size = get.option("window.size"),
  use.sex.chromosomes = FALSE,
  ignore.strand = TRUE
)

Arguments

bam.file	bath to the bam file to be analyzed already aligned to a reference genome
anno	annotation as a GRanges object with the CpG sites to be analyzed
log.path	location of the log file
cores	number of cores available for the analysis
window.size	window size used to restrict the concordance/discordance classification of each read pair DEFAULT: 50 as the maximum distance
use.sex.chromosomes	Flag indicating if scores are also to be computed for the sex chromosomes
ignore.strand	The ignore.strand parameter from the function findOverlaps

Value

qFDRP scores for the given annotation.

Author(s)

Michael Scherer

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