calculate.fdrp.score: calculate.fdrp.score

In MPIIComputationalEpigenetics/WSH_package: 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 FDRPs/qFDRPs (depending on how the options are set) for all CpG sites in the annotation from the reads provided by the bam file.

Usage

calculate.fdrp.score(
  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	CpG sites to be analyzed as a GRanges object
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

FDRP scores for the given annotation.

Author(s)

Michael Scherer

MPIIComputationalEpigenetics/WSH_package documentation built on Dec. 26, 2021, 8:42 a.m.