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

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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 <frohlich@bit.uni-bonn.de>
Date of publication
None
Maintainer
Holger Froehlich <frohlich@bit.uni-bonn.de>
License
GPL (>= 2)
Version
1.12.0

View on Bioconductor

Man pages

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.

Files in this package

GOSim/DESCRIPTION
GOSim/NAMESPACE
GOSim/R
GOSim/R/GOenrichment.R
GOSim/R/clusterEvaluation.R
GOSim/R/geneSimilarity.R
GOSim/R/general.R
GOSim/R/manifold_embedding.R
GOSim/R/norm.R
GOSim/R/normalize.kernel.R
GOSim/R/pca.R
GOSim/R/termSimilarity.R
GOSim/build
GOSim/build/vignette.rds
GOSim/data
GOSim/data/ICsBPhumanall.rda
GOSim/data/ICsCChumanall.rda
GOSim/data/ICsMFhumanall.rda
GOSim/inst
GOSim/inst/CITATION
GOSim/inst/doc
GOSim/inst/doc/GOSim.R
GOSim/inst/doc/GOSim.Rnw
GOSim/inst/doc/GOSim.pdf
GOSim/man
GOSim/man/GOenrichment.Rd
GOSim/man/IC.Rd
GOSim/man/calc.diffusion.kernel.Rd
GOSim/man/calcICs.Rd
GOSim/man/evaluateClustering.Rd
GOSim/man/filterGO.Rd
GOSim/man/getAncestors.Rd
GOSim/man/getChildren.Rd
GOSim/man/getDisjCommAnc.Rd
GOSim/man/getGOGraph.Rd
GOSim/man/getGOInfo.Rd
GOSim/man/getGeneFeatures.Rd
GOSim/man/getGeneFeaturesPrototypes.Rd
GOSim/man/getGeneSim.Rd
GOSim/man/getGeneSimPrototypes.Rd
GOSim/man/getMinimumSubsumer.Rd
GOSim/man/getOffsprings.Rd
GOSim/man/getParents.Rd
GOSim/man/getTermSim.Rd
GOSim/man/internal.Rd
GOSim/man/selectPrototypes.Rd
GOSim/man/setEnrichmentFactors.Rd
GOSim/man/setEvidenceLevel.Rd
GOSim/man/setOntology.Rd
GOSim/src
GOSim/src/Makevars
GOSim/src/OAWrapper.cpp
GOSim/src/hungarian2.c
GOSim/src/hungarian2.h
GOSim/vignettes
GOSim/vignettes/GOClusterExample.pdf
GOSim/vignettes/GOClustersil.pdf
GOSim/vignettes/GOExample.pdf
GOSim/vignettes/GOPCAExample.pdf
GOSim/vignettes/GOSim.Rnw
GOSim/vignettes/references.bib