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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("goProfiles")
AuthorAlex Sanchez, Jordi Ocana and Miquel Salicru
Bioconductor views Annotation GO GeneExpression GeneSetEnrichment GraphAndNetwork Microarray MultipleComparison Pathways Software
Date of publicationNone
MaintainerAlex Sanchez <asanchez@ub.edu>
LicenseGPL-2
Version1.38.0
http://eib.stat.ub.edu/goProfiles

View on Bioconductor

Functions

as.GOTerms.frame Man page
as.GOTerms.list Man page
basicProfile Man page
BioCpack2EntrezIDS Man page
BioCpack2Profiles Man page
BioCprobes2Entrez Man page
CD4GOTermsFrame Man page
CD4GOTermsList Man page
CD4LLids Man page
compareGeneLists Man page
compareGOProfiles Man page
compareProfilesLists Man page
compSummary Man page
diseaseIds Man page
dominantIds Man page
dominantIdsEBI Man page
dominantIdsNCBI Man page
drosophilaIds Man page
equivalentGOProfiles Man page
equivalentGOProfiles.default Man page
equivalentGOProfiles.ExpandedGOProfile Man page
equivalentGOProfiles.GOProfileHtest Man page
equivSummary Man page
expandedLevel Man page
expandedProfile Man page
expandTerm Man page
fisherGOProfiles Man page
fisherGOProfiles.BasicGOProfile Man page
fisherGOProfiles.ExpandedGOProfile Man page
fisherGOProfiles.matrix Man page
fisherGOProfiles.numeric Man page
fitGOProfile Man page
getAncestorsLst Man page
getGOLevel Man page
goProfiles Man page
goProfiles-package Man page
GOTermsFrame2GOTermsList Man page
GOTermsList Man page
hugoIds Man page
mergeProfilesLists Man page
michaudIds Man page
morbidmapIds Man page
omimIds Man page
ostrinIds Man page
plotProfiles Man page
printProfiles Man page
prostateIds Man page
recessiveIds Man page
recessiveIdsEBI Man page
recessiveIdsNCBI Man page
singh01EntrezIDs Man page
singh05EntrezIDs Man page
welsh01EntrezIDs Man page
welsh05EntrezIDs Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.