ChIPseqSet-class: Class '"ChIPseqSet"'

In epigenomix: Epigenetic and gene transcription data normalization and integration with mixture models

Description

A class for storing count data obtained from ChIP-seq experiments by counting the number of reads lying within regions. The class extends RangedSummarizedExperiment.

Objects from the Class

Objects can be created by calls of the form ChIPseqSet(chipVals=countDataMatrix, rowRanges=genomicRegions, colData=DataFrame(row.names=colnames(countDataMatrix)), ...). However, one will most likely create a ChIPseqSet object by calling summarizeReads.

Slots

metadata:

An optional list of arbitrary content describing the overall experiment.

rowRanges:

Object of class "GRanges" or "GRangesList" containing the genomic regions where the reads were counted.

colData:

Object of class "DataFrame" containing information on variable values of the samples. Some methods require the total library size of each sample stored in a column titled totalCounts.

assays:

Object of class SimpleList of a matrix, named chipVals containing the read counts per genomic region.

Extends

Class "RangedSummarizedExperiment", directly.

Methods

chipVals

signature(object = "ChIPseqSet"): Returns the matrix with read counts.

chipVals<-

signature(object = "ChIPseqSet", value = "matrix"): Sets the matrix with read counts.

cpm

signature(object = "ChIPseqSet", libSize, log2=FALSE, priorCount=0.1): Returns an object of ChIPseqSet with read counts standardized by library size - counts per million (cpm). If the library size is not given, the column sums of the given object are used. Cpm values are logarithmized after adding priorCounts, if log2 is TRUE.

Author(s)

Hans-Ulrich Klein ([e-mail])

See Also

summarizeReads, normalizeChIP

Examples

showClass("ChIPseqSet")

epigenomix documentation built on Nov. 8, 2020, 5:24 p.m.