compute.score.rnb: compute.score.rnb

Description Usage Arguments Value Author(s) Examples

View source: R/main.R

Description

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

Usage

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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

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