Computation of functional similarities between GO terms and gene products; GO enrichement analysis


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Documentation for package ‘GOSim’ version 1.1.3.2

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analyzeCluster Evaluate a given grouping of genes or GO terms.
calcICs Calculate information contents of GO terms.
calcTermSim internal functions
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.
getDensityFactor internal functions
getDepthFactor internal functions
getDisjAnc internal functions
getDisjCommAnc Get disjoint common ancestors.
getDisjCommAncSim internal functions
getEnrichedSim internal functions
getGeneFeaturesPrototypes Get feature vector representation of genes.
getGeneSim Compute functional similarity for genes.
getGeneSimPrototypes Compute functional similarity of genes with respect to a feature vector representation.
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.
getGOGraphsGenes (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.
getGSim internal functions
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.
GOenrichment GO enrichment analysis
GOGraph internal functions
IC Information content of GO terms
ICsBP Information content of GO terms
ICsBPIMP_IGI_IDA_IEP_IPI Information content of GO terms
ICsCCall Information content of GO terms
ICsCCIMP_IGI_IDA_IEP_IPI Information content of GO terms
ICsMFall Information content of GO terms
ICsMFIMP_IGI_IDA_IEP_IPI Information content of GO terms
initialize internal functions
internal internal functions
norm internal functions
pca internal functions
precomputeTermSims 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.