compute.score.GRanges: compute.score.GRanges

Description Usage Arguments Value Author(s) Examples

View source: R/main.R

Description

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

Usage

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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

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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/WSH_package documentation built on Oct. 19, 2021, 12:14 p.m.