calculate.pdr: calculate.pdr

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 PDRs for all analyzed CpG sites in the bam file of the corresponding sample

Usage

calculate.pdr(
  bam.file,
  anno,
  log.path = getwd(),
  cores = 1,
  window.size = unname(get.option("window.size")),
  max.reads = unname(get.option("max.reads")),
  mapq.filter = unname(get.option("mapq.filter")),
  coverage.threshold = unname(get.option("coverage.threshold")),
  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
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

PDR scores for the given annotation.

Author(s)

Michael Scherer

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