goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

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The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.

Author
Alex Sanchez, Jordi Ocana and Miquel Salicru
Date of publication
None
Maintainer
Alex Sanchez <asanchez@ub.edu>
License
GPL-2
Version
1.36.0
URLs

View on Bioconductor

Man pages

basicProfile
Builds basic functional profile
CD4ids
Entrez identifiers for CD4-TCells example
compareGeneLists
Compares two lists of genes by building (expanded) profiles...
compareGOProfiles
Comparison of lists of genes through their functional...
compareProfilesLists
Compares two of expanded profiles
compSummary
This function returns a brief summary of the comparison...
conversionFunctions
Functions to transformconvert objects between different types
drosophila
Entrez identifiers for genes related with an eye mutation in...
equivalentGOProfiles
Are two lists of genes equivalent in terms of their Gene...
equivSummary
This function returns a brief summary of the equivalence test...
expandedLevel
Function to create expanded levels which can contain GO Terms...
expandedProfile
Builds expanded profiles
fisherGOProfiles
GO Class-by-class Fisher tests in lists of genes...
fitGOProfile
Does a "sample" GO profile 'pn', observed in a sample of 'n'...
goProfiles-package
Performs Gene Ontology based analysis using Functional...
GOTermsList
Functions to create and manage lists of GO terms associated...
hugoIds
Entrez Identifiers obtained from the Human Genome...
mergeProfilesLists
Combines two lists of profiles into one
omimIds
Entrez identifiers for disease-related genes in the OMIM...
plotProfiles
Plot functional profiles
printProfiles
Print functional profiles
prostateIds
Prostate cancer-related genes

Files in this package

goProfiles/DESCRIPTION
goProfiles/NAMESPACE
goProfiles/R
goProfiles/R/BioCpack2EntrezIDS.R
goProfiles/R/BioCpack2Profiles.R
goProfiles/R/BioCprobes2Entrez.R
goProfiles/R/GOTermsFrame2GOTermsList.R
goProfiles/R/GOTermsList.R
goProfiles/R/as.ExpandedGOProfile.ExpandedGOProfile.R
goProfiles/R/as.ExpandedGOProfile.R
goProfiles/R/as.ExpandedGOProfile.default.R
goProfiles/R/as.GOTerms.frame.R
goProfiles/R/as.GOTerms.list.R
goProfiles/R/basicProfile.R
goProfiles/R/belongs.to.R
goProfiles/R/chiDisjoint.R
goProfiles/R/chiIntersect.R
goProfiles/R/chiPnP0Correct.R
goProfiles/R/chiRestrict.R
goProfiles/R/compSummary.R
goProfiles/R/compareGOProfiles.R
goProfiles/R/compareGeneLists.R
goProfiles/R/compareProfilesLists.R
goProfiles/R/completeMat.R
goProfiles/R/completeNames.R
goProfiles/R/contrMatrix.R
goProfiles/R/contractCol.R
goProfiles/R/contractedProfile.R
goProfiles/R/contrast.r
goProfiles/R/covGO.ExpandedGOProfile.R
goProfiles/R/covGO.R
goProfiles/R/covGO.default.R
goProfiles/R/coverage.r
goProfiles/R/dEuclid2.R
goProfiles/R/dgetGO.R
goProfiles/R/dimsGO.R
goProfiles/R/equivSummary.r
goProfiles/R/equivalentGOProfiles.R
goProfiles/R/estimProbPrecision.R
goProfiles/R/expandCol.R
goProfiles/R/expandNames.R
goProfiles/R/expandRndGO.R
goProfiles/R/expandTerm.R
goProfiles/R/expandedLevel.R
goProfiles/R/expandedProfile.R
goProfiles/R/fisherGOProfiles.R
goProfiles/R/fitGOProfile.R
goProfiles/R/frelGO.R
goProfiles/R/fullGOProfile.R
goProfiles/R/fullSetOfNames.R
goProfiles/R/generate.multinomial.R
goProfiles/R/geometricProfile.R
goProfiles/R/getAncestorsLst.R
goProfiles/R/getGOLevel.R
goProfiles/R/has.element.R
goProfiles/R/has.ngenes.attr.R
goProfiles/R/has.numGenes.attr.R
goProfiles/R/haveEntrezID.R
goProfiles/R/haveGO.R
goProfiles/R/idEuclid2.R
goProfiles/R/idEuclid2P0.R
goProfiles/R/internal.compareGOProf.R
goProfiles/R/internal.covGO.R
goProfiles/R/internal.enrich.R
goProfiles/R/internal.enrichProfile.R
goProfiles/R/internal.equivalentGOProf.R
goProfiles/R/internal.fitGOProf.R
goProfiles/R/internal.varDifStatPP0.R
goProfiles/R/internal.varDifStatPnQm.R
goProfiles/R/ipvalueP1Q1PQLinCombChisq.R
goProfiles/R/ipvaluePQLinCombChisq.R
goProfiles/R/ipvaluePnP0LinCombChisq.R
goProfiles/R/ipvaluePnPmLinCombChisq.R
goProfiles/R/lcombChisqParsOK.R
goProfiles/R/lenGO.R
goProfiles/R/meanICLength.R
goProfiles/R/mergeProfiles.R
goProfiles/R/mergeProfilesLists.R
goProfiles/R/multinomial.R
goProfiles/R/ngenes.BasicGOProfile.R
goProfiles/R/ngenes.ExpandedGOProfile.R
goProfiles/R/ngenes.default.R
goProfiles/R/ngenes.i.R
goProfiles/R/ngenes.matrix.R
goProfiles/R/ngenes.numeric.R
goProfiles/R/ngenes.r
goProfiles/R/niceProfile.R
goProfiles/R/normIntLength.R
goProfiles/R/plcombChisq.R
goProfiles/R/plotProfiles.R
goProfiles/R/printProfiles.R
goProfiles/R/pvalueExcludingLinCombChisq.R
goProfiles/R/pvalueIntersectLinCombChisq.R
goProfiles/R/pvaluePnP0LinCombChisq.R
goProfiles/R/pvalueRestrictLinCombChisq.R
goProfiles/R/qlcombChisq.R
goProfiles/R/rawProfile.R
goProfiles/R/reset.generation.multinomial.R
goProfiles/R/rlcombChisq.R
goProfiles/R/rndExpandedGOProfile.R
goProfiles/R/rndGO.R
goProfiles/R/seDifStatPP0.R
goProfiles/R/seDifStatPnQm.R
goProfiles/R/secondOrderMarginals.R
goProfiles/R/setN.multinomial.R
goProfiles/R/shortName.R
goProfiles/R/sigma.excluding.R
goProfiles/R/sigma.intersect.R
goProfiles/R/sigma.restrict.R
goProfiles/R/sum.and.R
goProfiles/R/sum.if.R
goProfiles/R/table2xs.R
goProfiles/R/toNumVec.R
goProfiles/R/varDifStatPP0.ExpandedGOProfile.R
goProfiles/R/varDifStatPP0.R
goProfiles/R/varDifStatPP0.default.R
goProfiles/R/varDifStatPnQm.R
goProfiles/R/vecProfile.R
goProfiles/build
goProfiles/build/vignette.rds
goProfiles/data
goProfiles/data/CD4Ids.rda
goProfiles/data/drosophila.rda
goProfiles/data/hugoIds.rda
goProfiles/data/omimIds.rda
goProfiles/data/prostateIds.rda
goProfiles/inst
goProfiles/inst/doc
goProfiles/inst/doc/goProfiles.R
goProfiles/inst/doc/goProfiles.Rnw
goProfiles/inst/doc/goProfiles.pdf
goProfiles/man
goProfiles/man/CD4ids.Rd
goProfiles/man/GOTermsList.Rd
goProfiles/man/basicProfile.Rd
goProfiles/man/compSummary.Rd
goProfiles/man/compareGOProfiles.Rd
goProfiles/man/compareGeneLists.Rd
goProfiles/man/compareProfilesLists.Rd
goProfiles/man/contractedProfile.rd
goProfiles/man/conversionFunctions.Rd
goProfiles/man/drosophila.Rd
goProfiles/man/equivSummary.Rd
goProfiles/man/equivalentGOProfiles.Rd
goProfiles/man/expandedLevel.Rd
goProfiles/man/expandedProfile.Rd
goProfiles/man/fisherGOProfiles.Rd
goProfiles/man/fitGOProfile.Rd
goProfiles/man/goProfiles-package.Rd
goProfiles/man/hugoIds.Rd
goProfiles/man/mergeProfilesLists.Rd
goProfiles/man/ngenes.rd
goProfiles/man/omimIds.Rd
goProfiles/man/plotProfiles.Rd
goProfiles/man/printProfiles.Rd
goProfiles/man/prostateIds.Rd
goProfiles/vignettes
goProfiles/vignettes/fancyhdr.sty
goProfiles/vignettes/goProfiles.Rnw