set.option: set.option

Description Usage Arguments Author(s) Examples

View source: R/main.R

Description

Change global options for WSH score calculation

Usage

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set.option(
  window.size = 50,
  mapq.filter = 35,
  max.reads = 40,
  min.overlap = 35,
  fdrp.type = "FDRP",
  coverage.threshold = 10,
  methclone.methylation.diff = 0,
  perl.path = "/usr/bin/perl",
  samtools.path = "/usr/bin"
)

Arguments

window.size

Window around the CpG site of interest to consider in FDRP and qFDRP calculation, the higher the value, the more likely it is to find heterogeneity

mapq.filter

mapq filter used to filter out low quality reads

max.reads

Maximum number of reads to be considered in FDRP and qFDRP calculation. The scores compute all pairs, therefore this is a crucial parameter for the running time of the calculation.

min.overlap

Miniumum overlap between two reads to consider it as a read pair in FDRP/qFDRP calculation in bp.

fdrp.type

FDRP type to be used: either FDRP or qFDRP

coverage.threshold

Coverage Threshold emloyed to select the sites in a RnBSet annotation that fullfill havin a coverage higher than this threshold

methclone.methylation.diff

Methylation difference parameter employed by the methclone software. Only sites are considered that have a methylation difference higher than this value in the methclone package.

perl.path

Path to an installation of perl on the machine

samtools.path

path to the directory where samtools is located in your machine

Author(s)

Michael Scherer

Examples

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get.option("coverage.threshold")
set.option(coverage.threshold=42)
get.option("coverage.threshold")

MPIIComputationalEpigenetics/WSHPackage documentation built on Oct. 22, 2021, 2:07 p.m.