ReadCountSet-class {SeqGSEA} | R Documentation

## Class `"ReadCountSet"`

### Description

ReadCountSet class

### Objects from the Class

Objects can be created by calls of the form `newReadCountSet`.

### Slots

`featureData_gene`:

  Object of class `"data.frame"`. Data for each genes.

`permute_NBstat_exon`:

  Object of class `"matrix"`. NB statistics of exons on the permutation data sets.

`permute_NBstat_gene`:

  Object of class `"matrix"`. NB statistics of genes on the permutation data sets.

`assayData`:

  Object of class `"AssayData"`. The read count data.

`phenoData`:

  Object of class `"AnnotatedDataFrame"`. Data for each samples.

`featureData`:

  Object of class `"AnnotatedDataFrame"`. Data for each exons.

`experimentData`:

  Object of class `"MIAxE"`. Experiment data.

`annotation`:

  Object of class `"character"`. Not used.

`protocolData`:

  Object of class `"AnnotatedDataFrame"`. Protocol information.

`.__classVersion__`:

  Object of class `"Versions"`. Version information.

### Methods

counts

  Get counts from a ReadCountSet object. See `counts`.

counts<-

  Set counts to a ReadCountSet object. See `counts`.

### Extends

Class `"eSet"`, directly.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

### See Also

`newReadCountSet`, `loadExonCountData`, `exonID`, `geneID`, `counts-methods`, `label`, `subsetByGenes`

### Examples

    showClass("ReadCountSet")

[Package SeqGSEA version 1.34.0 Index]