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| 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 | Get graphNEL object with leaves specified in the arguments. |
| 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. |
| 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. |