RepeatEpigenomeCollection-class: RepeatEpigenomeCollection Class

In MPIIComputationalEpigenetics/epiRepeatR: epiRepeatR

Description

A class for storing quantitative epigenetic data in repetitive elements of the genome

Usage

RepeatEpigenomeCollection(quantFns, sampleNames, markNames, annot,
  repRef = RepeatReference())

Arguments

quantFns

Vector of filenames which contains quantification results

Details

Multiple epigenetic marks are stored and each repetitive element (RE) in a given reference is assigned quantitative scores for each mark. A dataset of multiple samples can be annotated.

Slots

annot

Annotation for the samples in the dataset.

repRef

Repeat reference (of class RepeatReference)

samples

Samples contained in the dataset.

marks

epigenetic marks contained in the dataset.

markTypes

Annotation for the samples in the dataset.

epiQuant

Data structure for storing the quantifications of the epigenetic marks across marks and samples

Methods

getSamples,RepeatEpigenomeCollection-method

Return the sample indentifiers contained in the dataset.

getMarks,RepeatEpigenomeCollection-method

Return the epigenetic marks contained in the dataset.

getAnnot,RepeatEpigenomeCollection-method

Return the sample sample annotation table.

getSampleMarkTable,RepeatEpigenomeCollection-method

Return a table containing sample-mark combinations covered in the dataset.

getRepRef,RepeatEpigenomeCollection-method

Retrieve values of epigenetic quantifications for each RE in each sample.

getRepeatScores,RepeatEpigenomeCollection-method

Return the sample indentifiers contained in the dataset.

getRepeatCovg,RepeatEpigenomeCollection-method

Retrieve the number of reads covering each RE in each sample.

filterRepRefMeth,RepeatEpigenomeCollection-method

Filter RE that do not fulfill certain coverage criteria in all of the contained bisulfite datasets.

filterRepRefChip,RepeatEpigenomeCollection-method

Filter RE that do not fulfill certain coverage criteria in all of the contained enrichment datasets.

Author(s)

Fabian Mueller

Fabian Mueller

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