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Documentation for package `Category' version 2.2.3

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A C D E F G H I K M O P S T U

-- A --

annotation Accessors for HyperGResult Objects
annotation,GOHyperGParams-method Class "GOHyperGParams"
annotation,HyperGParams-method Class "HyperGParams"
annotation,HyperGResultBase-method Accessors for HyperGResult Objects
applyByCategory Apply a function to a vector of statistics, by category

-- C --

cateGOry Construct a category membership matrix 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
chrBandInciMat Create an incidence matrix mapping chromosome bands to genes
chrGraph Accessors for HyperGResult Objects
chrGraph,ChrMapHyperGResult-method Accessors for HyperGResult Objects
ChrMapHyperGParams-class Class "ChrMapHyperGParams"
ChrMapHyperGResult-class Class "ChrMapHyperGResult"
condGeneIdUniverse Accessors for HyperGResult Objects
condGeneIdUniverse,ChrMapHyperGResult-method Accessors for HyperGResult Objects
condGeneIdUniverse,HyperGResultBase-method Accessors for HyperGResult Objects
conditional Class "HyperGParams"
conditional,GOHyperGParams-method Class "GOHyperGParams"
conditional,HyperGParams-method Class "HyperGParams"
conditional<-,GOHyperGParams,logical-method Class "GOHyperGParams"

-- D --

description Accessors for HyperGResult Objects
description,HyperGResultBase-method Accessors for HyperGResult Objects

-- E --

expectedCounts Accessors for HyperGResult Objects
expectedCounts,ChrMapHyperGResult-method Accessors for HyperGResult Objects
expectedCounts,HyperGResult-method Accessors for HyperGResult Objects

-- F --

findAMstats Compute per category summary statistics

-- G --

geneCounts Accessors for HyperGResult Objects
geneCounts,HyperGResultBase-method Accessors for HyperGResult Objects
geneGoHyperGeoTest Hypergeometric Tests for GO (DEFUNCT)
geneIds Accessors for HyperGResult Objects
geneIds,HyperGParams-method Class "HyperGParams"
geneIds,HyperGResultBase-method Accessors for HyperGResult Objects
geneIds<-,HyperGParams,logical-method Class "HyperGParams"
geneIds<-,HyperGParams-method Class "HyperGParams"
geneIdsByCategory Accessors for HyperGResult Objects
geneIdsByCategory,HyperGResultBase-method Accessors for HyperGResult Objects
geneIdUniverse Accessors for HyperGResult Objects
geneIdUniverse,ChrMapHyperGResult-method Accessors for HyperGResult Objects
geneIdUniverse,HyperGResult-method Accessors for HyperGResult Objects
geneKeggHyperGeoTest Hypergeometric Tests for KEGG (DEFUNCT)
geneMappedCount Accessors for HyperGResult Objects
geneMappedCount,HyperGResultBase-method Accessors for HyperGResult Objects
getPathNames A function to print pathway names given their numeric id.
GOHyperGParams-class Class "GOHyperGParams"

-- H --

htmlReport Accessors for HyperGResult Objects
htmlReport,HyperGResultBase-method Accessors for HyperGResult Objects
HyperGParams-class Class "HyperGParams"
HyperGResult-accessors Accessors for HyperGResult Objects
HyperGResult-class Class "HyperGResult"
HyperGResultBase-class Class "HyperGResultBase"
hyperGTest Hypergeometric Test for association of categories and genes
hyperGTest,ChrMapHyperGParams-method Hypergeometric Test for association of categories and genes
hyperGTest,HyperGParams-method Hypergeometric Test for association of categories and genes

-- I --

initialize,HyperGParams-method Class "HyperGParams"
isConditional Class "HyperGParams"
isConditional,ChrMapHyperGResult-method Accessors for HyperGResult Objects
isConditional,HyperGParams-method Class "HyperGParams"
isConditional,HyperGResultBase-method Accessors for HyperGResult Objects

-- K --

KEGGHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"

-- M --

makeChrBandGraph Create a graph representing chromosome band annotation data
makeChrBandInciMat Create an incidence matrix mapping chromosome bands to genes
makeEBcontr A function to make the contrast vectors needed for EBarrays
makeValidParams Non-standard Generic for Checking Validity of Parameter Objects
makeValidParams,HyperGParams-method Class "HyperGParams"
MAPAmat Create an adjacency matrix for MAP

-- O --

oddsRatios Accessors for HyperGResult Objects
oddsRatios,ChrMapHyperGResult-method Accessors for HyperGResult Objects
oddsRatios,HyperGResult-method Accessors for HyperGResult Objects
ontology Class "HyperGParams"
ontology,GOHyperGParams-method Class "GOHyperGParams"
ontology,HyperGParams-method Class "HyperGParams"
ontology<-,GOHyperGParams,character-method Class "GOHyperGParams"

-- P --

PFAMHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
probes2MAP Map probe IDs to MAP regions.
probes2Path A function to map probe identifiers to pathways.
pvalueCutoff Accessors for HyperGResult Objects
pvalueCutoff,HyperGParams-method Class "HyperGParams"
pvalueCutoff,HyperGResultBase-method Accessors for HyperGResult Objects
pvalueCutoff<-,HyperGParams-method Class "HyperGParams"
pvalues Accessors for HyperGResult Objects
pvalues,ChrMapHyperGResult-method Accessors for HyperGResult Objects
pvalues,HyperGResult-method Accessors for HyperGResult Objects

-- S --

show,GOHyperGParams-method Class "GOHyperGParams"
show,HyperGParams-method Class "HyperGParams"
show,HyperGResultBase-method Class "HyperGResultBase"
sigCategories Accessors for HyperGResult Objects
sigCategories,HyperGResultBase-method Accessors for HyperGResult Objects
summary,HyperGResultBase-method Accessors for HyperGResult Objects

-- T --

testDirection Accessors for HyperGResult Objects
testDirection,HyperGParams-method Class "HyperGParams"
testDirection,HyperGResultBase-method Accessors for HyperGResult Objects
testDirection<-,HyperGParams-method Class "HyperGParams"
testName Accessors for HyperGResult Objects
testName,HyperGResultBase-method Accessors for HyperGResult Objects
ttperm A simple function to compute a permutation t-test.

-- U --

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 Accessors for HyperGResult Objects
universeCounts,HyperGResultBase-method Accessors for HyperGResult Objects
universeGeneIds Class "HyperGParams"
universeGeneIds,HyperGParams-method Class "HyperGParams"
universeMappedCount Accessors for HyperGResult Objects
universeMappedCount,HyperGResultBase-method Accessors for HyperGResult Objects