SeqGeneSet-class: Class '"SeqGeneSet"'

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

Description

SeqGeneSet class

Objects from the Class

Objects can be created by calls of the function newGeneSets.

Slots

name:

Object of class "character" the name of this gene set category

sourceFile:

Object of class "character" the source file of gene set category

geneList:

Object of class "character" the gene ID list indicating genes involved in this GSEA

GS:

Object of class "list" a list of gene indexes corresponding to geneList, each element in the list indicating which genes are in each gene set of this SeqGeneSet object

GSNames:

Object of class "character". Gene set names.

GSDescs:

Object of class "character". Gene set descriptions.

GSSize:

Object of class "numeric". Gene set sizes.

GSSizeMin:

Object of class "numeric". The minimum gene set size to be analyzed.

GSSizeMax:

Object of class "numeric". The maximum gene set size to be analyzed.

GS.Excluded:

Object of class "list". Gene sets excluded to be analyzed.

GSNames.Excluded:

Object of class "character". Gene set names excluded to be analyzed.

GSDescs.Excluded:

Object of class "character". Gene set descriptions excluded to be analyzed.

GSEA.ES:

Object of class "numeric". Enrichment scores.

GSEA.ES.pos:

Object of class "numeric". The positions where enrichment scores appear.

GSEA.ES.perm:

Object of class "matrix". The enrichment scores of the permutation data sets.

GSEA.score.cumsum:

Object of class "matrix". Running enrichment scores.

GSEA.normFlag:

Object of class "logical". Logical indicating whether GSEA.ES has been normalized.

GSEA.pval:

Object of class "numeric". P-values of each gene set.

GSEA.FWER:

Object of class "numeric". Family-wise error rate of each gene set.

GSEA.FDR:

Object of class "numeric". False discovery rate of each gene set.

sc.ES:

Object of class "numeric". Enrichment scores in scGSEA.

sc.ES.perm:

Object of class "matrix". The enrichment scores of the permutation data sets in scGSEA.

sc.normFlag:

Object of class "logical". Logical indicating whether sc.ES has been normalized in scGSEA.

scGSEA:

Object of class "logical". Whether or not used for scGSEA.

sc.pval:

Object of class "numeric". P-values of each gene set in scGSEA.

sc.FWER:

Object of class "numeric". Family-wise error rate of each gene set in scGSEA.

sc.FDR:

Object of class "numeric". False discovery rate of each gene set in scGSEA.

version:

Object of class "Versions". Version information.

Methods

[

Get a sub-list of gene sets, and return a SeqGeneSet object.

show

Show basic information of the SeqGeneSet object.

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

newGeneSets, size, geneSetNames, geneSetDescs, geneSetSize

Examples

showClass("SeqGeneSet")

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.