calculate.fdrp.score: calculate.fdrp.score

In schmic05/ISH_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 = get.option("WINDOW.SIZE"),
  use.sex.chromosomes = FALSE
)

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

Value

FDRP scores for the given annotation.

Author(s)

Michael Scherer

schmic05/ISH_package documentation built on March 18, 2021, 5:42 p.m.