| goProfiles-package | Performs Gene Ontology based analysis using Functional Profiles. |
| as.GOTerms.frame | Functions to transformconvert objects between different types |
| as.GOTerms.list | Functions to transformconvert objects between different types |
| basicProfile | Builds basic functional profile |
| BioCpack2EntrezIDS | Functions to transformconvert objects between different types |
| BioCpack2Profiles | Functions to transformconvert objects between different types |
| BioCprobes2Entrez | Functions to transformconvert objects between different types |
| CD4GOTermsFrame | Entrez identifiers for CD4-TCells example |
| CD4GOTermsList | Entrez identifiers for CD4-TCells example |
| CD4LLids | Entrez identifiers for CD4-TCells example |
| clustKidneyMF2 | Ready 2 cluster equivalence distance matrix obtained from the analysis of the "Kidney Dataset" at level 2 of the MF ontology |
| compareGeneLists | Compares two lists of genes by building (expanded) profiles and comparing them |
| compareGOProfiles | Comparison of lists of genes through their functional profiles |
| compareProfilesLists | Compares two of expanded profiles |
| compSummary | This function returns a brief summary of the comparison between two (expanded) profiles. |
| contractedProfile | Converts an expanded GO profile into a basic (contracted) GO profile |
| contractedProfile.default | Converts an expanded GO profile into a basic (contracted) GO profile |
| contractedProfile.ExpandedGOProfile | Converts an expanded GO profile into a basic (contracted) GO profile |
| diseaseIds | Entrez identifiers for disease-related genes in the OMIM database |
| dominantIds | Entrez identifiers for disease-related genes in the OMIM database |
| dominantIdsEBI | Entrez identifiers for disease-related genes in the OMIM database |
| dominantIdsNCBI | Entrez identifiers for disease-related genes in the OMIM database |
| drosophilaIds | Entrez identifiers for genes related with an eye mutation in drosophila |
| equivalentGOProfiles | Are two lists of genes equivalent in terms of their Gene Ontology profiles? |
| equivalentGOProfiles.default | Are two lists of genes equivalent in terms of their Gene Ontology profiles? |
| equivalentGOProfiles.ExpandedGOProfile | Are two lists of genes equivalent in terms of their Gene Ontology profiles? |
| equivalentGOProfiles.GOProfileHtest | Are two lists of genes equivalent in terms of their Gene Ontology profiles? |
| 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. |
| equivClust2pdf.equivClust | Save the graphical representation of objects of class 'equivClust' or 'iterEquivClust' as pdf files. |
| equivClust2pdf.iterEquivClust | 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. |
| expandedLevel | Function to create expanded levels which can contain GO Terms at different GO levels |
| expandedProfile | Builds expanded profiles |
| expandTerm | Function to create expanded levels which can contain GO Terms at different GO levels |
| fisherGOProfiles | GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles |
| fisherGOProfiles.BasicGOProfile | GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles |
| fisherGOProfiles.ExpandedGOProfile | GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles |
| fisherGOProfiles.matrix | GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles |
| fisherGOProfiles.numeric | 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? |
| getAncestorsLst | Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers |
| getGOLevel | Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers |
| goProfiles | Performs Gene Ontology based analysis using Functional Profiles. |
| GOTermsFrame2GOTermsList | Functions to transformconvert objects between different types |
| GOTermsList | Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers |
| 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 |
| michaudIds | Entrez identifiers for genes related with an eye mutation in drosophila |
| morbidmapIds | Entrez identifiers for disease-related genes in the OMIM database |
| ngenes | Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them) |
| ngenes.BasicGOProfile | Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them) |
| ngenes.default | Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them) |
| ngenes.ExpandedGOProfile | Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them) |
| ngenes.matrix | Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them) |
| ngenes.numeric | 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 |
| ostrinIds | Entrez identifiers for genes related with an eye mutation in drosophila |
| plotProfiles | Plot functional profiles |
| printProfiles | Print functional profiles |
| prostateIds | Prostate cancer-related genes |
| recessiveIds | Entrez identifiers for disease-related genes in the OMIM database |
| recessiveIdsEBI | Entrez identifiers for disease-related genes in the OMIM database |
| recessiveIdsNCBI | Entrez identifiers for disease-related genes in the OMIM database |
| singh01EntrezIDs | Prostate cancer-related genes |
| singh05EntrezIDs | Prostate cancer-related genes |
| welsh01EntrezIDs | Prostate cancer-related genes |
| welsh05EntrezIDs | Prostate cancer-related genes |