Category Analysis


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Documentation for package ‘Category’ version 2.12.1

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

-- A --

AffyDatPkg-class Class "DatPkg"
allGeneIds Class "ChrBandTree"
allGeneIds,ChrBandTree-method Class "ChrBandTree"
annotation Accessors for HyperGResult Objects
annotation,GOHyperGParams-method Class "GOHyperGParams"
annotation,HyperGParams-method Class "HyperGParams"
annotation,HyperGResultBase-method Accessors for HyperGResult Objects
annotation,LinearMParams-method Class "LinearMParams"
annotation,LinearMResultBase-method Class "LinearMResultBase"
annotation<-,HyperGParams,character-method Class "HyperGParams"
annotation<-,LinearMParams,character-method Class "LinearMParams"
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"
categoryName,LinearMParams-method Class "LinearMParams"
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
cb_children Create and Test Contingency Tables of Chromosome Band Annotations
cb_contingency Create and Test Contingency Tables of Chromosome Band Annotations
cb_parse_band_Hs Parse Homo Sapiens Chromosome Band Annotations
cb_parse_band_hsa Parse Homo Sapiens Chromosome Band Annotations
cb_parse_band_Mm Parse Mus Musculus Chromosome Band Annotations
cb_sigBands Create and Test Contingency Tables of Chromosome Band Annotations
cb_test Chromosome Band Tree-Based Hypothesis Testing
childrenOf Class "ChrBandTree"
childrenOf,ChrBandTree,character-method Class "ChrBandTree"
chrBandInciMat Create an incidence matrix mapping chromosome bands to genes
ChrBandTree-class Class "ChrBandTree"
ChrBandTreeFromGraph Create a new ChrBandTree object
chrGraph Accessors for HyperGResult Objects
chrGraph,ChrMapHyperGResult-method Accessors for HyperGResult Objects
chrGraph,ChrMapLinearMResult-method Class "ChrMapLinearMResult"
ChrMapHyperGParams-class Class "ChrMapHyperGParams"
ChrMapHyperGResult-class Class "ChrMapHyperGResult"
ChrMapLinearMParams-class Class "ChrMapLinearMParams"
ChrMapLinearMResult-class Class "ChrMapLinearMResult"
condGeneIdUniverse Accessors for HyperGResult Objects
condGeneIdUniverse,ChrMapHyperGResult-method Accessors for HyperGResult Objects
condGeneIdUniverse,ChrMapLinearMResult-method Class "ChrMapLinearMResult"
condGeneIdUniverse,HyperGResultBase-method Accessors for HyperGResult Objects
condGeneIdUniverse,LinearMResultBase-method Class "LinearMResultBase"
conditional Class "HyperGParams"
conditional,ChrMapHyperGParams-method Class "ChrMapHyperGParams"
conditional,ChrMapHyperGResult-method Class "ChrMapHyperGResult"
conditional,ChrMapLinearMParams-method Class "ChrMapLinearMParams"
conditional,GOHyperGParams-method Class "GOHyperGParams"
conditional,HyperGParams-method Class "HyperGParams"
conditional,HyperGResultBase-method Class "HyperGResultBase"
conditional,LinearMParams-method Class "LinearMParams"
conditional,LinearMResultBase-method Class "LinearMResultBase"
conditional<- Class "HyperGParams"
conditional<-,ChrMapHyperGParams,logical-method Class "ChrMapHyperGParams"
conditional<-,ChrMapLinearMParams,logical-method Class "ChrMapLinearMParams"
conditional<-,GOHyperGParams,logical-method Class "GOHyperGParams"

-- D --

DatPkg-class Class "DatPkg"
DatPkgFactory Class "DatPkg"
DatPkgFactory,character-method Class "DatPkg"
description Accessors for HyperGResult Objects
description,HyperGResultBase-method Accessors for HyperGResult Objects
description,LinearMResultBase-method Class "LinearMResultBase"

-- E --

effectSize Extract estimated effect sizes
effectSize,LinearMResult-method Class "LinearMResult"
exampleLevels Display a sample node from each level of a ChrBandTree object
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,ChrBandTree-method Class "ChrBandTree"
geneIds,HyperGParams-method Class "HyperGParams"
geneIds,HyperGResultBase-method Accessors for HyperGResult Objects
geneIds,LinearMParams-method Class "LinearMParams"
geneIds,LinearMResultBase-method Class "LinearMResultBase"
geneIds<- Class "HyperGParams"
geneIds<-,HyperGParams,ANY-method Class "HyperGParams"
geneIds<-,HyperGParams,logical-method Class "HyperGParams"
geneIds<-,LinearMParams,ANY-method Class "LinearMParams"
geneIdsByCategory Accessors for HyperGResult Objects
geneIdsByCategory,HyperGResultBase-method Accessors for HyperGResult Objects
geneIdsByCategory,LinearMResultBase-method Class "LinearMResultBase"
geneIdUniverse Accessors for HyperGResult Objects
geneIdUniverse,ChrMapHyperGResult-method Accessors for HyperGResult Objects
geneIdUniverse,HyperGResult-method Accessors for HyperGResult Objects
geneIdUniverse,LinearMResult-method Class "LinearMResult"
geneKeggHyperGeoTest Hypergeometric Tests for KEGG (DEFUNCT)
geneMappedCount Accessors for HyperGResult Objects
geneMappedCount,HyperGResultBase-method Accessors for HyperGResult Objects
geneMappedCount,LinearMResultBase-method Class "LinearMResultBase"
GeneSetCollectionDatPkg Class "DatPkg"
getPathNames A function to print pathway names given their numeric ID.
GO2AllProbes Class "DatPkg"
GO2AllProbes,DatPkg-method Class "DatPkg"
GO2AllProbes,GeneSetCollectionDatPkg-method Class "DatPkg"
GO2AllProbes,Org.XX.egDatPkg-method Class "DatPkg"
GO2AllProbes,YeastDatPkg-method Class "DatPkg"
GOHyperGParams-class Class "GOHyperGParams"
GSEAGOHyperGParams Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection
GSEAKEGGHyperGParams Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection
gseattperm Permutation p-values for GSEA

-- H --

htmlReport Accessors for HyperGResult Objects
htmlReport,HyperGResultBase-method Accessors for HyperGResult Objects
htmlReport,KEGGHyperGResult-method Accessors for HyperGResult Objects
htmlReport,PFAMHyperGResult-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
hyperGTest,KEGGHyperGParams-method Hypergeometric Test for association of categories and genes
hyperGTest,PFAMHyperGParams-method Hypergeometric Test for association of categories and genes

-- I --

ID2EntrezID Class "DatPkg"
ID2EntrezID,AffyDatPkg-method Class "DatPkg"
ID2EntrezID,ArabidopsisDatPkg-method Class "DatPkg"
ID2EntrezID,GeneSetCollectionDatPkg-method Class "DatPkg"
ID2EntrezID,Org.XX.egDatPkg-method Class "DatPkg"
ID2EntrezID,YeastDatPkg-method Class "DatPkg"
ID2GO Class "DatPkg"
ID2GO,DatPkg-method Class "DatPkg"
ID2GO,GeneSetCollectionDatPkg-method Class "DatPkg"
ID2KEGG Class "DatPkg"
ID2KEGG,DatPkg-method Class "DatPkg"
ID2KEGG,GeneSetCollectionDatPkg-method Class "DatPkg"
initialize,HyperGParams-method Class "HyperGParams"
isConditional Class "HyperGParams"
isConditional,ChrMapHyperGParams-method Class "ChrMapHyperGParams"
isConditional,ChrMapHyperGResult-method Accessors for HyperGResult Objects
isConditional,ChrMapLinearMResult-method Class "ChrMapLinearMResult"
isConditional,GOHyperGParams-method Class "GOHyperGParams"
isConditional,HyperGParams-method Class "HyperGParams"
isConditional,HyperGResultBase-method Accessors for HyperGResult Objects
isConditional,LinearMResultBase-method Class "LinearMResultBase"
isDBDatPkg,DatPkg-method Class "DatPkg"
isDBDatPkg,GeneSetCollectionDatPkg-method Class "DatPkg"

-- K --

KEGG2AllProbes Class "DatPkg"
KEGG2AllProbes,DatPkg-method Class "DatPkg"
KEGG2AllProbes,GeneSetCollectionDatPkg-method Class "DatPkg"
KEGGHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
KEGGHyperGResult-class Class "HyperGResult"

-- L --

level2nodes Class "ChrBandTree"
level2nodes,ChrBandTree,character-method Class "ChrBandTree"
level2nodes,ChrBandTree,numeric-method Class "ChrBandTree"
lgeneIds Class "ChrBandTree"
lgeneIds,ChrBandTree-method Class "ChrBandTree"
LinearMParams-class Class "LinearMParams"
LinearMResult-class Class "LinearMResult"
LinearMResultBase-class Class "LinearMResultBase"
linearMTest A linear model-based test to detect enrichment of unusual genes in categories
linearMTest,LinearMParams-method A linear model-based test to detect enrichment of unusual genes in categories

-- 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 incidence matrix mapping chromosome bands to genes

-- N --

NewChrBandTree Create a new ChrBandTree object

-- 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<- Class "HyperGParams"
ontology<-,GOHyperGParams,character-method Class "GOHyperGParams"
Org.XX.egDatPkg-class Class "DatPkg"

-- P --

parentOf Class "ChrBandTree"
parentOf,ChrBandTree,character-method Class "ChrBandTree"
PFAMHyperGParams-class Class "KEGGHyperGParams" and "PFAMHyperGParams"
PFAMHyperGResult-class Class "HyperGResult"
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,LinearMParams-method Class "LinearMParams"
pvalueCutoff,LinearMResultBase-method Class "LinearMResultBase"
pvalueCutoff<- Class "HyperGParams"
pvalueCutoff<-,HyperGParams-method Class "HyperGParams"
pvalueCutoff<-,LinearMParams-method Class "LinearMParams"
pvalues Accessors for HyperGResult Objects
pvalues,ChrMapHyperGResult-method Accessors for HyperGResult Objects
pvalues,HyperGResult-method Accessors for HyperGResult Objects
pvalues,LinearMResult-method Class "LinearMResult"

-- S --

show,ChrBandTree-method Class "ChrBandTree"
show,GOHyperGParams-method Class "GOHyperGParams"
show,HyperGParams-method Class "HyperGParams"
show,HyperGResultBase-method Class "HyperGResultBase"
show,LinearMParams-method Class "LinearMParams"
show,LinearMResultBase-method Class "LinearMResultBase"
sigCategories Accessors for HyperGResult Objects
sigCategories,HyperGResultBase-method Accessors for HyperGResult Objects
sigCategories,LinearMResultBase-method Class "LinearMResultBase"
summary,HyperGResultBase-method Accessors for HyperGResult Objects
summary,KEGGHyperGResult-method Accessors for HyperGResult Objects
summary,LinearMResultBase-method Class "LinearMResultBase"
summary,PFAMHyperGResult-method Accessors for HyperGResult Objects

-- T --

testDirection Accessors for HyperGResult Objects
testDirection,HyperGParams-method Class "HyperGParams"
testDirection,HyperGResultBase-method Accessors for HyperGResult Objects
testDirection,LinearMParams-method Class "LinearMParams"
testDirection,LinearMResultBase-method Class "LinearMResultBase"
testDirection<- Class "HyperGParams"
testDirection<-,HyperGParams-method Class "HyperGParams"
testDirection<-,LinearMParams-method Class "LinearMParams"
testName Accessors for HyperGResult Objects
testName,HyperGResultBase-method Accessors for HyperGResult Objects
testName,LinearMResultBase-method Class "LinearMResultBase"
treeLevels Class "ChrBandTree"
treeLevels,ChrBandTree-method Class "ChrBandTree"
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
universeCounts,LinearMResultBase-method Class "LinearMResultBase"
universeGeneIds Class "HyperGParams"
universeGeneIds,HyperGParams-method Class "HyperGParams"
universeGeneIds,LinearMParams-method Class "LinearMParams"
universeMappedCount Accessors for HyperGResult Objects
universeMappedCount,HyperGResultBase-method Accessors for HyperGResult Objects
universeMappedCount,LinearMResultBase-method Class "LinearMResultBase"

-- Y --

YeastDatPkg-class Class "DatPkg"