ReadCountSet-class: Class '"ReadCountSet"'

Description Objects from the Class Slots Methods Extends Author(s) References See Also Examples

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

1
showClass("ReadCountSet")

SeqGSEA documentation built on May 31, 2017, 3:19 p.m.