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Documentation for package `Category' version 2.0.3

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annotation,GOHyperGParams-method Class "GOHyperGParams"
annotation,HyperGParams-method Class "HyperGParams"
annotation,HyperGResultBase-method Class "HyperGResultBase"
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.
categoryName Class "HyperGParams"
categoryName,GOHyperGParams-method Class "GOHyperGParams"
categoryName,HyperGParams-method Class "HyperGParams"
categoryToEntrezBuilder Return a list mapping category ids to Entrez Gene ids
categoryToEntrezBuilder,GOHyperGParams-method Return a list mapping category ids to Entrez Gene ids
categoryToEntrezBuilder,KEGGHyperGParams-method Return a list mapping category ids to Entrez Gene ids
categoryToEntrezBuilder,PFAMHyperGParams-method Return a list mapping category ids to Entrez Gene ids
conditional Class "HyperGParams"
conditional,GOHyperGParams-method Class "GOHyperGParams"
conditional,HyperGParams-method Class "HyperGParams"
conditional<-,GOHyperGParams,logical-method Class "GOHyperGParams"
description,HyperGResultBase-method Class "HyperGResultBase"
expectedCounts Class "HyperGResult"
expectedCounts,HyperGResult-method Class "HyperGResult"
findAMstats Compute per category summary statistics
geneCounts Class "HyperGResult"
geneCounts,HyperGResult-method Class "HyperGResult"
geneGoHyperGeoTest Hypergeometric Tests for GO
geneIds Class "HyperGResultBase"
geneIds,HyperGParams-method Class "HyperGParams"
geneIds,HyperGResultBase-method Class "HyperGResultBase"
geneIds<-,HyperGParams,logical-method Class "HyperGParams"
geneIds<-,HyperGParams-method Class "HyperGParams"
geneKeggHyperGeoTest Hypergeometric Tests for KEGG
geneMappedCount Class "HyperGResultBase"
geneMappedCount,HyperGResultBase-method Class "HyperGResultBase"
getPathNames A function to print pathway names given their numeric id.
GOHyperGParams-class Class "GOHyperGParams"
htmlReport Class "HyperGResultBase"
htmlReport,HyperGResultBase-method Class "HyperGResultBase"
HyperGParams-class Class "HyperGParams"
HyperGResult-class Class "HyperGResult"
HyperGResultBase-class Class "HyperGResultBase"
hyperGTest Hypergeometric Test for association of categories and genes
hyperGTest,HyperGParams-method Hypergeometric Test for association of categories and genes
isConditional Class "HyperGParams"
isConditional,HyperGParams-method Class "HyperGParams"
isConditional,HyperGResultBase-method Class "HyperGResultBase"
KEGGHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
makeEBcontr A function to make the contrast vectors needed for EBarrays
MAPAmat Create an adjacency matrix for MAP
oddsRatios Class "HyperGResult"
oddsRatios,HyperGResult-method Class "HyperGResult"
ontology Class "HyperGParams"
ontology,GOHyperGParams-method Class "GOHyperGParams"
ontology,HyperGParams-method Class "HyperGParams"
ontology<-,GOHyperGParams,character-method Class "GOHyperGParams"
PFAMHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
probes2MAP Map probe IDs to MAP regions.
probes2Path A function to map probe identifiers to pathways.
pvalueCutoff Class "HyperGResultBase"
pvalueCutoff,HyperGParams-method Class "HyperGParams"
pvalueCutoff,HyperGResultBase-method Class "HyperGResultBase"
pvalueCutoff<-,HyperGParams-method Class "HyperGParams"
pvalues Class "HyperGResult"
pvalues,HyperGResult-method Class "HyperGResult"
show,GOHyperGParams-method Class "GOHyperGParams"
show,HyperGResultBase-method Class "HyperGResultBase"
summary,HyperGResultBase-method Class "HyperGResultBase"
testDirection Class "HyperGResultBase"
testDirection,HyperGParams-method Class "HyperGParams"
testDirection,HyperGResultBase-method Class "HyperGResultBase"
testDirection<-,HyperGParams-method Class "HyperGParams"
testName Class "HyperGResultBase"
testName,HyperGResultBase-method Class "HyperGResultBase"
ttperm A simple function to compute a permutation t-test.
universeBuilder Return a vector of gene identifiers with category annotations
universeBuilder,GOHyperGParams-method Return a vector of gene identifiers with category annotations
universeBuilder,KEGGHyperGParams-method Return a vector of gene identifiers with category annotations
universeBuilder,PFAMHyperGParams-method Return a vector of gene identifiers with category annotations
universeCounts Class "HyperGResult"
universeCounts,HyperGResult-method Class "HyperGResult"
universeGeneIds Class "HyperGParams"
universeGeneIds,HyperGParams-method Class "HyperGParams"
universeMappedCount Class "HyperGResult"
universeMappedCount,HyperGResult-method Class "HyperGResult"