set.option: set.option

In MPIIComputationalEpigenetics/WSHPackage: R package for the calculation of the following Within-Sample Heterogeneity Scores in Bisulfite Sequencing Data: FDRP, qFDRP, PDR, Epipolymorphism, Methylation Entropy and MHL

Description

Change global options for WSH score calculation

Usage

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

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

MPIIComputationalEpigenetics/WSHPackage documentation built on Dec. 14, 2021, 11:49 a.m.