getRepeatCovg-RepeatEpigenomeCollection-method: getRepeatCovg-methods

In MPIIComputationalEpigenetics/epiRepeatR: epiRepeatR

Description

Retrieve the number of reads covering each RE in each sample

Usage

## S4 method for signature 'RepeatEpigenomeCollection'
getRepeatCovg(.Object, mark,
  dropEmptySamples = FALSE, type = "numReads")

Arguments

.Object	RepeatEpigenomeCollection object
mark	Epigenetic mark for which the coverage information is retrieved
dropEmptySamples	Logical indicating whether samples in which the mark is not present should be dropped
type	Coverage type. Should be one of the following: "numReads": [default] number of reads covering a RE "maxCpGcov": [DNAmeth only] maximum number of reads covering a single CpG "numInstances": [DNAmeth from genome methylation calls only] number of repeat instances in the genome

Value

A matrix of dimension numRE X numSamples containing coverage values

Author(s)

Fabian Mueller

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