enrichment {GSEA} R Documentation

do GSEA enrichment analysis

Description

<br /> Gene set enrichment analysis (GSEA) (also called functional <br /> enrichment analysis or pathway enrichment analysis) is a <br /> method to identify classes of genes or proteins that are <br /> over-represented in a large set of genes or proteins, and <br /> may have an association with disease phenotypes. The method <br /> uses statistical approaches to identify significantly enriched <br /> or depleted groups of genes. Transcriptomics technologies <br /> and proteomics results often identify thousands of genes <br /> which are used for the analysis.

Usage

enrichment(background, geneSet,
    expression = NULL,
    cut.size = 3,
    outputAll = TRUE,
    resize = -1,
    showProgress = FALSE,
    ... = NULL);

Arguments

background

a Background model or @T:SMRUCC.genomics.Analysis.HTS.GSEA.KnowledgeBase.Metabolism.Metpa.metpa

geneSet

expression

args

the additional argument list that may be used,

for metpa background model, topo parameter will be used for specific the network topology impact score source, value of the topo parameter could be dgr or rbc. [as list]

Details

the expression value could be the raw expression mean value, different expression foldchange value for the group comparision, or other related gene set sort scores.

Authors

gseakit

Value

this function returns data object of type EnrichmentResult.

clr value class

Examples

[Package GSEA version 1.0.0.0 Index]