CD4LLids                Entrez identifiers for CD4-TCells example
GOTermsList             Functions to create and manage lists of GO
                        terms associated with a vector of 'Entrez'
                        identifiers
as.GOTerms.frame        Functions to transformconvert objects between
                        different types
basicProfile            Builds basic functional profile
clustKidneyMF2          Ready 2 cluster equivalence distance matrix
                        obtained from the analysis of the "Kidney
                        Dataset" at level 2 of the MF ontology
compSummary             This function returns a brief summary of the
                        comparison between two (expanded) profiles.
compareGOProfiles       Comparison of lists of genes through their
                        functional profiles
compareGeneLists        Compares two lists of genes by building
                        (expanded) profiles and comparing them
compareProfilesLists    Compares two of expanded profiles
contractedProfile       Converts an expanded GO profile into a basic
                        (contracted) GO profile
drosophilaIds           Entrez identifiers for genes related with an
                        eye mutation in drosophila
equivClust              For a given level (2, 3, ...) in a GO ontology
                        (BP, MF or CC), compute the equivalence
                        threshold distance matrix and generate a
                        dendrogram from it.
equivClust2pdf          Save the graphical representation of objects of
                        class 'equivClust' or 'iterEquivClust' as pdf
                        files.
equivSummary            This function returns a brief summary of the
                        equivalence test between two profiles.
equivalentGOProfiles    Are two lists of genes equivalent in terms of
                        their Gene Ontology profiles?
expandedLevel           Function to create expanded levels which can
                        contain GO Terms at different GO levels
expandedProfile         Builds expanded profiles
fisherGOProfiles        GO Class-by-class Fisher tests in lists of
                        genes characterized by their functional
                        profiles
fitGOProfile            Does a "sample" GO profile 'pn', observed in a
                        sample of 'n' genes, fit a "population" or
                        "model" p0?
goProfiles-package      Performs Gene Ontology based analysis using
                        Functional Profiles.
hugoIds                 Entrez Identifiers obtained from the Human
                        Genome Organization
iterEquivClust          For each combination of the specified levels in
                        the choosen GO ontologies, compute the
                        equivalence threshold distance matrix and
                        generate a dendrogram from it.
kidneyGeneLists         Gene-lists related to kidney transplantation
                        rejection
mergeProfilesLists      Combines two lists of profiles into one
ngenes                  Returns the number of genes that lead to this
                        GO profile (an object of class
                        ExpandedGOProfile, BasicGOProfile or
                        assimilable to them)
omimIds                 Entrez identifiers for disease-related genes in
                        the OMIM database
plotProfiles            Plot functional profiles
printProfiles           Print functional profiles
prostateIds             Prostate cancer-related genes
