GOenrichment {GOSim} | R Documentation |
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, ...).
GOenrichment (allpvalues, fdr=0.05, cutoff=0.01)
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 |
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 |
Holger Froehlich
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
analyzeCluster
, evaluateClustering
## 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)