ChIPseqSet-class {epigenomix} | R Documentation

## Class `"ChIPseqSet"`

### 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 (hklein@broadinstitute.org)

### See Also

`summarizeReads`, `normalizeChIP`

### Examples

    showClass("ChIPseqSet")

[Package epigenomix version 1.27.1 Index]