rnb.calculate.qfdrp: rnb.calculate.qfdrp

Description Usage Arguments Value Author(s) Examples

View source: R/connect_RnBeads.R

Description

This function calculates the qFDRP scores for a given RnBSet and a bam file containing the reads.

Usage

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rnb.calculate.qfdrp(
  rnb.set,
  bam.path,
  log.path = getwd(),
  cores = 1,
  use.sex.chromosomes = FALSE,
  ...
)

Arguments

rnb.set

RnBSet object containing the CpG sites for which calculation should be conducted

bam.path

path to the bam file containing the reads

log.path

path to the log directory, if not existing it is created

cores

cores available for the analysis

use.sex.chromosomes

Flag indicating if scores are also to be computed for the sex chromosomes

...

Further parameters passed to calculate.qfdrp

Value

qFDRP scores for the CpG sites in the RnBSet with a higher coverage than COVERAGE.THRESHOLD

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 <- rnb.calculate.qfdrp(rnb.set=example.rnb.set,bam.path=example.bam)

## End(Not run)

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