GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Version 1.14.0

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

Browse man pages Browse package API and functions Browse package files

AuthorHolger Froehlich <frohlich@bit.uni-bonn.de>
Bioconductor views Clustering GO Pathways Software
Date of publicationNone
MaintainerHolger Froehlich <frohlich@bit.uni-bonn.de>
LicenseGPL (>= 2)
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GOSim")

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.

Functions

GOGraph Man page Source code
GOenrichment Man page Source code
IC Man page
ICshumanBPall Man page
ICshumanCCall Man page
ICshumanMFall Man page
analyzeCluster Man page
calc.diffusion.kernel Man page Source code
calcICs Man page Source code
calcTermSim Man page Source code Source code
classificationModelSignalTrans_dme Man page
classificationModelSignalTrans_hsa Man page
classificationModel_dme Man page
evaluateClustering Man page Source code
filterGO Man page Source code
getAncestors Man page Source code
getChildren Man page Source code
getDensityFactor Man page Source code
getDepthFactor Man page Source code
getDisjAnc Man page Source code
getDisjCommAnc Man page Source code
getDisjCommAncSim Man page Source code
getEnrichedSim Man page Source code
getGIC Source code
getGOGraph Man page Source code
getGOGraphsGenes Man page Source code
getGOInfo Man page Source code
getGSim Man page Source code
getGeneFeatures Man page Source code
getGeneFeatures.internal Source code
getGeneFeaturesPrototypes Man page Source code
getGeneSim Man page Source code
getGeneSimPrototypes Man page Source code
getMinimumSubsumer Man page Source code
getOffsprings Man page Source code
getParents Man page Source code
getTermSim Man page Source code
getWeightedDotSim Source code
initialize Man page Source code
internal Man page
load.diffusion.kernel Man page Source code
norm Man page Source code
normalize.kernel Source code
pca Man page Source code
precomputeTermSims Man page Source code
selectPrototypes Man page Source code
setEnrichmentFactors Man page Source code
setEvidenceLevel Man page Source code
setOntology Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/GOenrichment.R
R/clusterEvaluation.R
R/geneSimilarity.R
R/general.R
R/manifold_embedding.R
R/norm.R
R/normalize.kernel.R
R/pca.R
R/termSimilarity.R
build
build/vignette.rds
data
data/ICsBPhumanall.rda
data/ICsCChumanall.rda
data/ICsMFhumanall.rda
inst
inst/CITATION
inst/doc
inst/doc/GOSim.R
inst/doc/GOSim.Rnw
inst/doc/GOSim.pdf
man
man/GOenrichment.Rd
man/IC.Rd
man/calc.diffusion.kernel.Rd
man/calcICs.Rd
man/evaluateClustering.Rd
man/filterGO.Rd
man/getAncestors.Rd
man/getChildren.Rd
man/getDisjCommAnc.Rd
man/getGOGraph.Rd
man/getGOInfo.Rd
man/getGeneFeatures.Rd
man/getGeneFeaturesPrototypes.Rd
man/getGeneSim.Rd
man/getGeneSimPrototypes.Rd
man/getMinimumSubsumer.Rd
man/getOffsprings.Rd
man/getParents.Rd
man/getTermSim.Rd
man/internal.Rd
man/selectPrototypes.Rd
man/setEnrichmentFactors.Rd
man/setEvidenceLevel.Rd
man/setOntology.Rd
src
src/Makevars
src/OAWrapper.cpp
src/hungarian2.c
src/hungarian2.h
vignettes
vignettes/GOClusterExample.pdf
vignettes/GOClustersil.pdf
vignettes/GOExample.pdf
vignettes/GOPCAExample.pdf
vignettes/GOSim.Rnw
vignettes/references.bib
GOSim documentation built on May 20, 2017, 9:19 p.m.