applyByCategory | Apply a function to a vector of statistics, by category |
cateGOry | Construct a category membership data structure from a list of gene identifiers and their annotated GO categories. |
categoryToEntrezBuilder | Return a list mapping category ids to Entrez Gene ids |
categoryToEntrezBuilder,GeneGoHyperGeoTestParams-method | Return a list mapping category ids to Entrez Gene ids |
categoryToEntrezBuilder,GeneKeggHyperGeoTestParams-method | Return a list mapping category ids to Entrez Gene ids |
findAMstats | Compute per category summary statistics |
geneCategoryHyperGeoTest | Test for overrepresentation of category terms in a set of genes |
geneCategoryHyperGeoTest,GeneCategoryHyperGeoTestParams-method | Test for overrepresentation of category terms in a set of genes |
GeneCategoryHyperGeoTestParams-class | Class "GeneCategoryHyperGeoTestParams" |
GeneCategoryHyperGeoTestResult-class | Class "GeneCategoryHyperGeoTestResult" |
geneGoHyperGeoTest | Hypergeometric Tests for GO |
GeneGoHyperGeoTestParams-class | Class "GeneGoHyperGeoTestParams" |
geneKeggHyperGeoTest | Hypergeometric Tests for KEGG |
GeneKeggHyperGeoTestParams-class | Class "GeneKeggHyperGeoTestParams" |
getPathNames | A function to print pathway names given their numeric id. |
GOHyperG | Hypergeometric Tests for GO |
makeEBcontr | A function to make the contrast vectors needed for EBarrays |
MAPAmat | Create an adjacency matrix for MAP |
probes2MAP | Map probe IDs to MAP regions. |
probes2Path | A function to map probe identifiers to pathways. |
show,GeneCategoryHyperGeoTestResult-method | Class "GeneCategoryHyperGeoTestResult" |
show,GeneGoHyperGeoTestParams-method | Class "GeneGoHyperGeoTestParams" |
ttperm | A simple function to compute a permutation t-test. |
universeBuilder | Return a vector of gene identifiers with category annotations |
universeBuilder,GeneGoHyperGeoTestParams-method | Return a vector of gene identifiers with category annotations |
universeBuilder,GeneKeggHyperGeoTestParams-method | Return a vector of gene identifiers with category annotations |