rnb.calculate.qfdrp: rnb.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 a given RnBSet and a bam file containing the reads.

Usage

rnb.calculate.qfdrp(
  rnb.set,
  bam.path,
  log.path = getwd(),
  cores = 1,
  use.sex.chromosomes = FALSE,
  ...
)

Arguments

rnb.set	RnBSet object containing the CpG sites for which calculation should be conducted
bam.path	path to the bam file containing the reads
log.path	path to the log directory, if not existing it is created
cores	cores available for the analysis
use.sex.chromosomes	Flag indicating if scores are also to be computed for the sex chromosomes
...	Further parameters passed to calculate.qfdrp

Value

qFDRP scores for the CpG sites in the RnBSet with a higher coverage than COVERAGE.THRESHOLD

Author(s)

Michael Scherer

Examples

## Not run: 
example.rnb.set <- system.file(file.path("extData","small_rnbSet.zip"),package="WSH")
example.bam <- system.file(file.path("extData","small_example.bam"),package="WSH")
fdrp <- rnb.calculate.qfdrp(rnb.set=example.rnb.set,bam.path=example.bam)

## End(Not run)

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