filterRepRefMeth-RepeatEpigenomeCollection-method: filterRepRefMeth-methods

In MPIIComputationalEpigenetics/epiRepeatR: epiRepeatR

Description

Given a RepeatEpigenomeCollection object, remove repeats that do not fulfill the coverage criteria in any sample

Usage

## S4 method for signature 'RepeatEpigenomeCollection'
filterRepRefMeth(.Object,
  minReads = getConfigElement("plotRepTree.meth.minReads"),
  minCpGs = getConfigElement("plotRepTree.meth.minCpGs"),
  minCpGcov = getConfigElement("meth.minCpGcov"),
  covgType = "numReads")

Arguments

.Object	RepeatEpigenomeCollection object
minReads	threshold for the minimum number of reads required to cover a repeat
minCpGs	threshold for the minimum number of CpGs that must be contained in a repeat
minCpGcov	threshold specifying that mininum number of reads that must cover at least one CpG in the repeat in order for it to be retained
covgType	type of read coverage to be applied (important for filtering via minReads). See getRepeatCovg,RepeatEpigenomeCollection-method for possible values.

Details

A repeat must fulfill the criteria in all samples in order to be retained

Value

modified RepeatEpigenomeCollection object

Author(s)

Fabian Mueller

MPIIComputationalEpigenetics/epiRepeatR documentation built on March 22, 2021, 11:09 p.m.