Entry: IC
Aliases: IC ICsBP ICsBPIMP_IGI_IDA_IEP_IPI ICsCCall ICsCCIMP_IGI_IDA_IEP_IPI ICsMFall ICsMFIMP_IGI_IDA_IEP_IPI
Keywords: datasets
Description: Information content of GO terms
URL: ../../../library/GOSim/html/IC.html

Entry: calcICs
Aliases: calcICs
Keywords: file
Description: Calculate information contents of GO terms.
URL: ../../../library/GOSim/html/calcICs.html

Entry: evaluateClustering
Aliases: evaluateClustering
Keywords: file
Description: Evaluate a given grouping of genes or GO terms.
URL: ../../../library/GOSim/html/evaluateClustering.html

Entry: filterGO
Aliases: filterGO
Keywords: file
Description: Filter GO.
URL: ../../../library/GOSim/html/filterGO.html

Entry: getAncestors
Aliases: getAncestors
Keywords: file
Description: get list of ALL ancestors associated to each GO term
URL: ../../../library/GOSim/html/getAncestors.html

Entry: getChildren
Aliases: getChildren
Keywords: file
Description: Get a list of all direct children of each GO term.
URL: ../../../library/GOSim/html/getChildren.html

Entry: getDisjCommAnc
Aliases: getDisjCommAnc
Keywords: file
Description: Get disjoint common ancestors.
URL: ../../../library/GOSim/html/getDisjCommAnc.html

Entry: getGOGraph
Aliases: getGOGraph
Keywords: file
Description: Get graphNEL object with leaves specified in the arguments.
URL: ../../../library/GOSim/html/getGOGraph.html

Entry: getGOInfo
Aliases: getGOInfo
Keywords: file
Description: Obtain GO terms and their description for a list of genes.
URL: ../../../library/GOSim/html/getGOInfo.html

Entry: getGeneFeaturesPrototypes
Aliases: getGeneFeaturesPrototypes
Keywords: file
Description: Get feature vector representation of genes.
URL: ../../../library/GOSim/html/getGeneFeaturesPrototypes.html

Entry: getGeneSim
Aliases: getGeneSim
Keywords: file
Description: Compute functional similarity for genes.
URL: ../../../library/GOSim/html/getGeneSim.html

Entry: getGeneSimPrototypes
Aliases: getGeneSimPrototypes
Keywords: file
Description: Compute functional similarity of genes with respect to a feature vector representation.
URL: ../../../library/GOSim/html/getGeneSimPrototypes.html

Entry: getMinimumSubsumer
Aliases: getMinimumSubsumer
Keywords: file
Description: Compute minimum subsumer of two GO terms.
URL: ../../../library/GOSim/html/getMinimumSubsumer.html

Entry: getOffsprings
Aliases: getOffsprings
Keywords: file
Description: Get all offspring associated with one or more GO term
URL: ../../../library/GOSim/html/getOffsprings.html

Entry: getParents
Aliases: getParents
Keywords: file
Description: Get direct parents for each GO term.
URL: ../../../library/GOSim/html/getParents.html

Entry: getTermSim
Aliases: getTermSim
Keywords: file
Description: Get pairwise GO term similarities.
URL: ../../../library/GOSim/html/getTermSim.html

Entry: internal
Aliases: internal calcTermSim getDensityFactor getDepthFactor getDisjAnc getDisjCommAncSim getEnrichedSim getGSim precomputeTermSims initialize pca norm
Keywords: file
Description: internal functions
URL: ../../../library/GOSim/html/internal.html

Entry: selectPrototypes
Aliases: selectPrototypes
Keywords: file
Description: Heuristic selection of prototypes and dimensionality reduction of feature vectors.
URL: ../../../library/GOSim/html/selectPrototypes.html

Entry: setEnrichmentFactors
Aliases: setEnrichmentFactors
Keywords: file
Description: Set the depth and densitiy enrichment factors for GO term similarity.
URL: ../../../library/GOSim/html/setEnrichmentFactors.html

Entry: setEvidenceLevel
Aliases: setEvidenceLevel
Keywords: file
Description: Specifies to use only GO terms with given evidence codes.
URL: ../../../library/GOSim/html/setEvidenceLevel.html

Entry: setOntology
Aliases: setOntology
Keywords: file
Description: Set an ontology as base for subsequent computations.
URL: ../../../library/GOSim/html/setOntology.html
