This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis
|Author||Holger Froehlich <email@example.com>|
|Date of publication||None|
|Maintainer||Holger Froehlich <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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.