Man pages for GOSim
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
| calc.diffusion.kernel | Calculation and loading of diffusion kernel matrices |
| calcICs | Calculate information contents of GO terms. |
| 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. |
| getDisjCommAnc | Get disjoint common ancestors. |
| getGeneFeatures | Get simple feature vector representation of genes |
| getGeneFeaturesPrototypes | Get feature vector representation of genes relative to... |
| getGeneSim | Compute functional similarity for genes |
| getGeneSimPrototypes | Compute functional similarity of genes with respect to a... |
| getGOGraph | (1) Get GO graph with specified GO terms at its leave; (2)... |
| getGOInfo | Obtain GO terms and their description for a list of genes. |
| 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 |
| IC | Information content of GO terms |
| internal | internal functions |
| selectPrototypes | Heuristic selection of prototypes and dimensionality... |
| setEnrichmentFactors | Set the depth and densitiy enrichment factors for GO term... |
| setEvidenceLevel | Specifies to use only GO terms with given evidence codes. |
| setOntology | Set an ontology as base for subsequent computations. |
