getRepeatScores-RepeatEpigenomeCollection-method: getRepeatScores-methods

Description Usage Arguments Value Author(s)

Description

Retrieve values of epigenetic quantifications for each RE in each sample

Usage

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## S4 method for signature 'RepeatEpigenomeCollection'
getRepeatScores(.Object, mark,
  dropEmptySamples = FALSE, minCpGcov = getConfigElement("meth.minCpGcov"))

Arguments

.Object

RepeatEpigenomeCollection object

mark

Epigenetic mark for which the score information is retrieved

dropEmptySamples

Logical indicating whether samples in which the mark is not present should be dropped

minCpGcov

[DNAmeth only] number of reads covering each CpG in order for it to be considered in the mean methylation level

Value

A matrix of dimension numRE X numSamples containing scores. Scores are mean methylation levels for DNA methylation and log2 of the fold change for enrichment based methods.

Author(s)

Fabian Mueller


MPIIComputationalEpigenetics/epiRepeatR documentation built on July 24, 2018, 10:10 p.m.