Category Analysis


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Documentation for package `Category' version 1.4.1

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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