GOenrichment            GO enrichment analysis
IC                      Information content of GO terms
calc.diffusion.kernel   Calculation and loading of diffusion kernel
                        matrices
calcICs                 Calculate information contents of GO terms.
evaluateClustering      Evaluate a given grouping of genes or GO terms.
filterGO                Filter GO.
getAncestors            get list of ALL ancestors associated to each GO
                        term
getChildren             Get a list of all direct children of each GO
                        term.
getDisjCommAnc          Get disjoint common ancestors.
getGOGraph              (1) Get GO graph with specified GO terms at its
                        leave; (2) Get GO Graph with GO terms at leaves
                        associated to one or several genes of interest.
getGOInfo               Obtain GO terms and their description for a
                        list of genes.
getGeneFeatures         Get simple feature vector representation of
                        genes
getGeneFeaturesPrototypes
                        Get feature vector representation of genes
                        relative to prototype genes
getGeneSim              Compute functional similarity for genes
getGeneSimPrototypes    Compute functional similarity of genes with
                        respect to a feature vector representation.
getMinimumSubsumer      Compute minimum subsumer of two GO terms.
getOffsprings           Get all offspring associated with one or more
                        GO term
getParents              Get direct parents for each GO term.
getTermSim              Get pairwise GO term similarities.
internal                internal functions
selectPrototypes        Heuristic selection of prototypes and
                        dimensionality reduction of feature vectors.
setEnrichmentFactors    Set the depth and densitiy enrichment factors
                        for GO term similarity.
setEvidenceLevel        Specifies to use only GO terms with given
                        evidence codes.
setOntology             Set an ontology as base for subsequent
                        computations.
