GOenrichment {GOSim}R Documentation

GO enrichment analysis

Description

This function performs a GO enrichment analysis using topGO. The analysis relies on the ranking of the genes according to some test statistic (p-values, t-statistic, z-statistic, ...).

Usage

GOenrichment (allpvalues, fdr=0.05, cutoff=0.01)

Arguments

allpvalues vector of (multiple testing corrected) p-values with names as Entrez gene IDs.
fdr FDR significance cutoff
cutoff significance cutoff for GO enrichment analysis

Value

GOTerms list of significant GO terms and their description
p.values vector of p-values for significant GO terms
genes list of genes associated to each GO term

Author(s)

Holger Froehlich

References

Adrian Alexa, J"org Rahnenf"uhrer, Thomas Lengauer: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, 2006, 22(13):1600-1607

See Also

analyzeCluster, evaluateClustering

Examples

        ## Not run: 
       
        setOntology("BP")
        gomap <- get("gomap",env=GOSimEnv)
        allgenes = sample(names(gomap), 1000) # suppose these are all genes
        allpvalues = runif(1000) # an these are their pvalues
        names(allpvalues) = allgenes
        if(require(topGO) & require(annotate))
                GOenrichment(allpvalues) # GO enrichment analysis
        
## End(Not run)

[Package GOSim version 1.1.3.2 Index]