gseaAnalysis: Perform a GSEA analysis of a list of genes

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Performs a GSEA analysis of a list of genes using the package topGO (see References).

Usage

gseaAnalysis(hitVector, whichOnto)

Arguments

hitVector	a named hit vector as generated by hitselectionZscore or hitselectionPval
whichOnto	One of the three GO ontologies: "biological_process", "molecular_function" or "cellular_component"

Value

A table containing the enriched GO terms and their significance.

References

A. Alexa, J. Rahnenfuhrer and T. Lengauer. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics, 22(13):1600-1607, 2006

Adrian Alexa and Jorg Rahnenfuhrer (2006). topGO: Enrichment analysis for Gene Ontology. R package version 1.4.0.

See Also

Ttest

Examples

data(scoredDataset1, package="RNAither")
data(pValVec1, package="RNAither")

##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Hits1", 0.1, 
"GeneName", "pvalue_testfile1.txt")
hitVector1 <- scoredHits1[[2]]
gseaTable <- gseaAnalysis(hitVector1, "biological_process")

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.