# Computation of functional similarities between GO terms and gene products; GO enrichment analysis

## Documentation for package ‘GOSim’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

analyzeCluster | GO enrichment analysis
calc.diffusion.kernel | Calculation and loading of diffusion kernel matrices
calcICs | Calculate information contents of GO terms.
calcTermSim | internal functions
classificationModelSignalTrans_dme | internal functions
classificationModelSignalTrans_hsa | internal functions
classificationModel_dme | 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
getGeneFeatures | Get simple feature vector representation of genes
getGeneFeaturesPrototypes | Get feature vector representation of genes relative to prototype genes
getGeneSim | Compute functional similarity for genes
getGeneSimPrototypes | Compute functional similarity of genes with respect to a feature vector representation.
getGOGraph | (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.
getGOGraphsGenes | (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.
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.
GOenrichment | GO enrichment analysis
GOGraph | internal functions
IC | Information content of GO terms
ICshumanBPall | Information content of GO terms
ICshumanCCall | Information content of GO terms
ICshumanMFall | Information content of GO terms
initialize | internal functions
internal | internal functions
load.diffusion.kernel | Calculation and loading of diffusion kernel matrices
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.