| 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 |
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