compute.score.GRanges: compute.score.GRanges

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 GRanges object and a bam file containing the reads.

Usage

compute.score.GRanges(
  bam.file,
  range,
  score = "qfdrp",
  use.sex.chromosomes = FALSE,
  ...
)

Arguments

bam.file	path to bam file containing the reads
range	GRanges object containing the annotation
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

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

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