compute.score: compute.score

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

Generic function to call, passes its arugments either to compute.score.rnb or compute.score.GRanges.

Usage

compute.score(
  bam.file,
  ...,
  score = "qfdrp",
  use.sex.chromosomes = FALSE,
  ignore.strand = TRUE
)

Arguments

bam.file	path to bam file containing the reads
...	additional arugment. Either RnBSet, GRanges or empty (only for Epipolymorphism and Entropy)
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
ignore.strand	The ignore.strand parameter from the function findOverlaps

Value

data frame containing the annotation and the computed WSH scores

Author(s)

Michael Scherer

Examples

load(system.file(file.path("extData","example_GRanges.RData"),package="WSH"))
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(bam.file=example.bam,example.GRanges,score="fdrp")
qfdrp <- compute.score(bam.file=example.bam,example.rnb.set,score="qfdrp")

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