compute.score: compute.score

Description Usage Arguments Value Author(s) Examples

View source: R/main.R

Description

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

Usage

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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

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