ReadCountSet-class: Class '"ReadCountSet"'

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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, [e-mail]

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")

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.