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GOSim (version 1.6.0)

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

Description

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

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Version

Monthly Downloads

41

Version

1.6.0

License

GPL (>= 2)

Maintainer

Holger Froehlich

Last Published

February 15th, 2017

Functions in GOSim (1.6.0)

getDisjCommAnc

Get disjoint common ancestors.
setEnrichmentFactors

Set the depth and densitiy enrichment factors for GO term similarity.
getAncestors

get list of ALL ancestors associated to each GO term
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.
getChildren

Get a list of all direct children of each GO term.
setEvidenceLevel

Specifies to use only GO terms with given evidence codes.
setOntology

Set an ontology as base for subsequent computations.
getGeneFeatures

Get simple feature vector representation of genes
internal

internal functions
calc.diffusion.kernel

Calculation and loading of diffusion kernel matrices
clusterEvaluation

Evaluate a given grouping of genes or GO terms.
filterGO

Filter GO.
getOffsprings

Get all offspring associated with one or more GO term
getParents

Get direct parents for each GO term.
GOenrichment

GO enrichment analysis
calcICs

Calculate information contents of GO terms.
IC

Information content of GO terms
getGeneFeaturesPrototypes

Get feature vector representation of genes relative to prototype genes
getGOInfo

Obtain GO terms and their description for a list of genes.
getGeneSim

Compute functional similarity for genes
getMinimumSubsumer

Compute minimum subsumer of two GO terms.