Man pages for GOSim
Computation of functional similarities between GO terms and gene products; GO enrichment analysis

calc.diffusion.kernelCalculation and loading of diffusion kernel matrices
calcICsCalculate information contents of GO terms.
evaluateClusteringEvaluate a given grouping of genes or GO terms.
filterGOFilter GO.
getAncestorsget list of ALL ancestors associated to each GO term
getChildrenGet a list of all direct children of each GO term.
getDisjCommAncGet disjoint common ancestors.
getGeneFeaturesGet simple feature vector representation of genes
getGeneFeaturesPrototypesGet feature vector representation of genes relative to...
getGeneSimCompute functional similarity for genes
getGeneSimPrototypesCompute functional similarity of genes with respect to a...
getGOGraph(1) Get GO graph with specified GO terms at its leave; (2)...
getGOInfoObtain GO terms and their description for a list of genes.
getMinimumSubsumerCompute minimum subsumer of two GO terms.
getOffspringsGet all offspring associated with one or more GO term
getParentsGet direct parents for each GO term.
getTermSimGet pairwise GO term similarities.
GOenrichmentGO enrichment analysis
ICInformation content of GO terms
internalinternal functions
selectPrototypesHeuristic selection of prototypes and dimensionality...
setEnrichmentFactorsSet the depth and densitiy enrichment factors for GO term...
setEvidenceLevelSpecifies to use only GO terms with given evidence codes.
setOntologySet an ontology as base for subsequent computations.
GOSim documentation built on Nov. 17, 2017, 1:24 p.m.