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 |
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? |
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 |
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 |