SeqGeneSet-class: Class '"SeqGeneSet"'

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

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, 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

newGeneSets, size, geneSetNames, geneSetDescs, geneSetSize

Examples

1
showClass("SeqGeneSet")

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