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. |