gseaAnalysis {RNAither} | R Documentation

## Perform a GSEA analysis of a list of genes

### 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")

[Package RNAither version 2.28.0 Index]