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


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Documentation for package ‘GOSim’ version 1.2

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analyzeCluster GO enrichment analysis
calc.diffusion.kernel Calculation and loading of diffusion kernel matrices
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
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
ICsflyBPall Information content of GO terms
ICsflyCCall Information content of GO terms
ICsflyMFall Information content of GO terms
ICshumanBPall Information content of GO terms
ICshumanCCall Information content of GO terms
ICshumanMFall Information content of GO terms
ICsmalariaBPall Information content of GO terms
ICsmalariaCCall Information content of GO terms
ICsmalariaMFall Information content of GO terms
ICsmouseBPall Information content of GO terms
ICsmouseCCall Information content of GO terms
ICsmouseMFall Information content of GO terms
ICsratBPall Information content of GO terms
ICsratCCall Information content of GO terms
ICsratMFall Information content of GO terms
ICsyeastBPall Information content of GO terms
ICsyeastCCall Information content of GO terms
ICsyeastMFall 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.