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 |

http://eib.stat.ub.edu/goProfiles |

**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

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

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