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 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.

cut.size

the minimum number of the member genes that a functional cluster should have, the clusters with fewer members than this cutoff will be removed from the enrichment analysis. Default 3. [as integer]

outputAll

keeps all of the clusters in the result table even if the cluster has no intersection with the input gene set? Default TRUE. [as boolean]

resize

the size of the input gene set that is used as the n of the hypergeometric test. Value less than or equals to zero means using the length of the geneSet vector. Default -1. [as integer]

showProgress

prints the progress message? Default FALSE. [as boolean]

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.

permutations parameter will be used for specific the permutation times of the GSEA method when the expression parameter is not missing, default 1000. [as list]

env

the R# runtime environment. [as Environment]

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

an array of the EnrichmentResult objects, which is sorted by the FDR value in ascending order.

clr value class

Examples

[Package GSEA version 1.0.0.0 Index]