Get direct parents for each GO term.
Get a list of all direct children of each GO term.
GO enrichment analysis
Filter GO.
Calculation and loading of diffusion kernel matrices
Information content of GO terms
Set an ontology as base for subsequent computations.
Get simple feature vector representation of genes
Compute functional similarity of genes with respect to a feature vector representation.
Obtain GO terms and their description for a list of genes.
Evaluate a given grouping of genes or GO terms.
getGeneFeaturesPrototypes
Get feature vector representation of genes relative to prototype genes
Compute minimum subsumer of two GO terms.
(1) Get GO graph with specified GO terms at its leave; (2) Get GO Graph with GO terms at leaves associated to one or several genes of interest.
Calculate information contents of GO terms.
Get disjoint common ancestors.
Specifies to use only GO terms with given evidence codes.
Get all offspring associated with one or more GO term
Get pairwise GO term similarities.
internal functions
get list of ALL ancestors associated to each GO term
Set the depth and densitiy enrichment factors for GO term
similarity.
Compute functional similarity for genes
Heuristic selection of prototypes and dimensionality reduction of feature vectors.