enrichment {GSEA} R Documentation

do GSEA enrichment analysis

Description


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

geneSet

a given geneset id list

expression

the expression value of the given gene set. this parameter could be missing. default use the fisher test enrichment method for the given gene set when the expression vector is missing. GSEA method will be applied for the enrichment analysis if this parameter is not missing.

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]