compute.score.rnb: compute.score.rnb

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

Main function to compute WSH scores based on a input RnBSet and a bam file containing the reads.

Usage

compute.score.rnb(
  bam.file,
  rnb.set,
  score = "qfdrp",
  use.sex.chromosomes = use.sex.chromosomes,
  ...
)

Arguments

bam.file	path to bam file containing the reads
rnb.set	path to RnBSet contaning methylation, coverage and sample meta information
score	The WSH score which should be computed, needs to be one of fdrp,qfdrp,pdr,epipolymorphism, entropy or mhl
use.sex.chromosomes	Flag indicating if scores are also to be computed for the sex chromosomes
...	Further parameters passed to calculate.*

Value

data frame containing the annotation and the computed WSH scores

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 <- compute.score.rnb(bam.file=example.bam,rnb.set=example.rnb.set)

## End(Not run)

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