AffyDatPkg-class	DatPkg-class
allGeneIds	ChrBandTree-class
allGeneIds,ChrBandTree-method	ChrBandTree-class
annotation	HyperGResult-accessors
annotation,GOHyperGParams-method	GOHyperGParams-class
annotation,HyperGParams-method	HyperGParams-class
annotation,HyperGResultBase-method	HyperGResult-accessors
annotation,LinearMParams-method	LinearMParams-class
annotation,LinearMResultBase-method	LinearMResultBase-class
annotation,OBOHyperGParams-method	OBOHyperGParams-class
annotation<-,HyperGParams,character-method	HyperGParams-class
annotation<-,LinearMParams,character-method	LinearMParams-class
applyByCategory	applyByCategory
ArabidopsisDatPkg-class	DatPkg-class
bottomup_tree_visitor	tree_visitor
cateGOry	cateGOryMatrix
Category-defunct	Category-defunct
categoryName	HyperGParams-class
categoryName,GOHyperGParams-method	GOHyperGParams-class
categoryName,HyperGParams-method	HyperGParams-class
categoryName,LinearMParams-method	LinearMParams-class
categoryName,OBOHyperGParams-method	OBOHyperGParams-class
categoryToEntrezBuilder	categoryToEntrezBuilder
categoryToEntrezBuilder,GOHyperGParams-method	categoryToEntrezBuilder
categoryToEntrezBuilder,KEGGHyperGParams-method	categoryToEntrezBuilder
categoryToEntrezBuilder,OBOHyperGParams-method	categoryToEntrezBuilder
categoryToEntrezBuilder,PFAMHyperGParams-method	categoryToEntrezBuilder
cb_children	cb_contingency
cb_contingency	cb_contingency
cb_parse_band_Hs	cb_parse_band_Hs
cb_parse_band_hsa	Category-defunct
cb_parse_band_Mm	cb_parse_band_Mm
cb_sigBands	cb_contingency
cb_test	cb_test
childrenOf	ChrBandTree-class
childrenOf,ChrBandTree,character-method	ChrBandTree-class
chrBandInciMat	Category-defunct
ChrBandTree-class	ChrBandTree-class
ChrBandTreeFromGraph	NewChrBandTree
chrGraph	HyperGResult-accessors
chrGraph,ChrMapHyperGResult-method	HyperGResult-accessors
chrGraph,ChrMapLinearMResult-method	ChrMapLinearMResult-class
ChrMapHyperGParams-class	ChrMapHyperGParams-class
ChrMapHyperGResult-class	ChrMapHyperGResult-class
ChrMapLinearMParams-class	ChrMapLinearMParams-class
ChrMapLinearMResult-class	ChrMapLinearMResult-class
condGeneIdUniverse	Category-defunct
conditional	HyperGParams-class
conditional,ChrMapHyperGParams-method	ChrMapHyperGParams-class
conditional,ChrMapHyperGResult-method	ChrMapHyperGResult-class
conditional,GOHyperGParams-method	GOHyperGParams-class
conditional,HyperGParams-method	HyperGParams-class
conditional,HyperGResultBase-method	HyperGResultBase-class
conditional,LinearMParams-method	LinearMParams-class
conditional,LinearMResultBase-method	LinearMResultBase-class
conditional,OBOHyperGParams-method	OBOHyperGParams-class
conditional<-	HyperGParams-class
conditional<-,ChrMapHyperGParams,logical-method	ChrMapHyperGParams-class
conditional<-,GOHyperGParams,logical-method	GOHyperGParams-class
conditional<-,LinearMParams,logical-method	LinearMParams-class
conditional<-,OBOHyperGParams,logical-method	OBOHyperGParams-class
DatPkg-class	DatPkg-class
DatPkgFactory	DatPkg-class
DatPkgFactory,character-method	DatPkg-class
DatPkgFactory,ChipDb-method	DatPkg-class
DatPkgFactory,OBOCollection,GeneSetCollection-method	DatPkg-class
DatPkgFactory,OrgDb-method	DatPkg-class
description	HyperGResult-accessors
description,HyperGResultBase-method	HyperGResult-accessors
description,LinearMResultBase-method	LinearMResultBase-class
effectSize	effectSize
effectSize,LinearMResult-method	LinearMResult-class
exampleLevels	exampleLevels
expectedCounts	HyperGResult-accessors
expectedCounts,ChrMapHyperGResult-method	HyperGResult-accessors
expectedCounts,HyperGResult-method	HyperGResult-accessors
findAMstats	findAMstats
geneCounts	HyperGResult-accessors
geneCounts,HyperGResultBase-method	HyperGResult-accessors
geneGoHyperGeoTest	Category-defunct
geneIds	HyperGResult-accessors
geneIds,ChrBandTree-method	ChrBandTree-class
geneIds,HyperGParams-method	HyperGParams-class
geneIds,HyperGResultBase-method	HyperGResult-accessors
geneIds,LinearMParams-method	LinearMParams-class
geneIds,LinearMResultBase-method	LinearMResultBase-class
geneIds<-	HyperGParams-class
geneIds<-,HyperGParams,ANY-method	HyperGParams-class
geneIds<-,HyperGParams,logical-method	HyperGParams-class
geneIds<-,LinearMParams,ANY-method	LinearMParams-class
geneIdsByCategory	HyperGResult-accessors
geneIdsByCategory,HyperGResultBase-method	HyperGResult-accessors
geneIdsByCategory,LinearMResultBase-method	LinearMResultBase-class
geneIdUniverse	HyperGResult-accessors
geneIdUniverse,ChrMapHyperGResult-method	HyperGResult-accessors
geneIdUniverse,HyperGResult-method	HyperGResult-accessors
geneIdUniverse,LinearMResultBase-method	LinearMResultBase-class
geneKeggHyperGeoTest	Category-defunct
geneMappedCount	HyperGResult-accessors
geneMappedCount,HyperGResultBase-method	HyperGResult-accessors
geneMappedCount,LinearMResultBase-method	LinearMResultBase-class
GeneSetCollectionDatPkg	DatPkg-class
getPathNames	getPathNames
GO2AllProbes	DatPkg-class
GO2AllProbes,DatPkg-method	DatPkg-class
GO2AllProbes,GeneSetCollectionDatPkg-method	DatPkg-class
GO2AllProbes,Org.XX.egDatPkg-method	DatPkg-class
GO2AllProbes,YeastDatPkg-method	DatPkg-class
GOHyperGParams-class	GOHyperGParams-class
GSEAGOHyperGParams	GSEAGOHyperGParams
GSEAKEGGHyperGParams	GSEAGOHyperGParams
gseattperm	gseattperm
hg_test_factory	local_test_factory
htmlReport	HyperGResult-accessors
htmlReport,HyperGResultBase-method	HyperGResult-accessors
htmlReport,KEGGHyperGResult-method	HyperGResult-accessors
htmlReport,PFAMHyperGResult-method	HyperGResult-accessors
hyperg	hyperg
hyperg,character-method	hyperg
hyperg,list-method	hyperg
HyperGParams-class	HyperGParams-class
HyperGResult-accessors	HyperGResult-accessors
HyperGResult-class	HyperGResult-class
HyperGResultBase-class	HyperGResultBase-class
hyperGTest	hyperGTest
hyperGTest,ChrMapHyperGParams-method	hyperGTest
hyperGTest,HyperGParams-method	hyperGTest
hyperGTest,KEGGHyperGParams-method	hyperGTest
hyperGTest,PFAMHyperGParams-method	hyperGTest
ID2EntrezID	DatPkg-class
ID2EntrezID,AffyDatPkg-method	DatPkg-class
ID2EntrezID,ArabidopsisDatPkg-method	DatPkg-class
ID2EntrezID,GeneSetCollectionDatPkg-method	DatPkg-class
ID2EntrezID,Org.XX.egDatPkg-method	DatPkg-class
ID2EntrezID,YeastDatPkg-method	DatPkg-class
ID2GO	DatPkg-class
ID2GO,DatPkg-method	DatPkg-class
ID2GO,GeneSetCollectionDatPkg-method	DatPkg-class
ID2KEGG	DatPkg-class
ID2KEGG,DatPkg-method	DatPkg-class
ID2KEGG,GeneSetCollectionDatPkg-method	DatPkg-class
initialize,HyperGParams-method	HyperGParams-class
isConditional	Category-defunct
isDBDatPkg,DatPkg-method	DatPkg-class
isDBDatPkg,GeneSetCollectionDatPkg-method	DatPkg-class
KEGG2AllProbes	DatPkg-class
KEGG2AllProbes,DatPkg-method	DatPkg-class
KEGG2AllProbes,GeneSetCollectionDatPkg-method	DatPkg-class
KEGGHyperGParams-class	KEGGHyperGParams-class
KEGGHyperGResult-class	HyperGResult-class
level2nodes	ChrBandTree-class
level2nodes,ChrBandTree,character-method	ChrBandTree-class
level2nodes,ChrBandTree,numeric-method	ChrBandTree-class
lgeneIds	ChrBandTree-class
lgeneIds,ChrBandTree-method	ChrBandTree-class
LinearMParams-class	LinearMParams-class
LinearMResult-class	LinearMResult-class
LinearMResultBase-class	LinearMResultBase-class
linearMTest	linearMTest
linearMTest,LinearMParams-method	linearMTest
local_test_factory	local_test_factory
makeChrBandGraph	makeChrBandGraph
makeChrBandGSC	MAPAmat
makeChrBandInciMat	MAPAmat
makeEBcontr	makeEBcontr
makeValidParams	makeValidParams
makeValidParams,HyperGParams-method	HyperGParams-class
MAPAmat	MAPAmat
NewChrBandTree	NewChrBandTree
OBOCollectionDatPkg	DatPkg-class
OBOCollectionDatPkg-class	DatPkg-class
OBOHyperGParams	OBOHyperGParams-class
OBOHyperGParams-class	OBOHyperGParams-class
oddsRatios	HyperGResult-accessors
oddsRatios,ChrMapHyperGResult-method	HyperGResult-accessors
oddsRatios,HyperGResult-method	HyperGResult-accessors
ontology	HyperGParams-class
ontology,GOHyperGParams-method	GOHyperGParams-class
ontology,HyperGParams-method	HyperGParams-class
ontology<-	HyperGParams-class
ontology<-,GOHyperGParams,character-method	GOHyperGParams-class
Org.XX.egDatPkg-class	DatPkg-class
organism,DatPkg-method	DatPkg-class
organism,GeneSetCollectionDatPkg-method	DatPkg-class
organism,HyperGParams-method	HyperGParams-class
organism,HyperGResult-method	HyperGResult-accessors
parentOf	ChrBandTree-class
parentOf,ChrBandTree,character-method	ChrBandTree-class
PFAMHyperGParams-class	KEGGHyperGParams-class
PFAMHyperGResult-class	HyperGResult-class
probes2MAP	probes2MAP
probes2Path	probes2Path
pvalueCutoff	HyperGResult-accessors
pvalueCutoff,HyperGParams-method	HyperGParams-class
pvalueCutoff,HyperGResultBase-method	HyperGResult-accessors
pvalueCutoff,LinearMParams-method	LinearMParams-class
pvalueCutoff,LinearMResultBase-method	LinearMResultBase-class
pvalueCutoff<-	HyperGParams-class
pvalueCutoff<-,HyperGParams-method	HyperGParams-class
pvalueCutoff<-,LinearMParams-method	LinearMParams-class
pvalues	HyperGResult-accessors
pvalues,ChrMapHyperGResult-method	HyperGResult-accessors
pvalues,HyperGResult-method	HyperGResult-accessors
pvalues,LinearMResult-method	LinearMResult-class
show,ChrBandTree-method	ChrBandTree-class
show,GOHyperGParams-method	GOHyperGParams-class
show,HyperGParams-method	HyperGParams-class
show,HyperGResultBase-method	HyperGResultBase-class
show,LinearMParams-method	LinearMParams-class
show,LinearMResultBase-method	LinearMResultBase-class
show,OBOHyperGParams-method	OBOHyperGParams-class
sigCategories	HyperGResult-accessors
sigCategories,HyperGResultBase-method	HyperGResult-accessors
sigCategories,LinearMResultBase-method	LinearMResultBase-class
summary,HyperGResultBase-method	HyperGResult-accessors
summary,KEGGHyperGResult-method	HyperGResult-accessors
summary,LinearMResult-method	LinearMResult-class
summary,LinearMResultBase-method	LinearMResultBase-class
summary,PFAMHyperGResult-method	HyperGResult-accessors
testDirection	HyperGResult-accessors
testDirection,HyperGParams-method	HyperGParams-class
testDirection,HyperGResultBase-method	HyperGResult-accessors
testDirection,LinearMParams-method	LinearMParams-class
testDirection,LinearMResultBase-method	LinearMResultBase-class
testDirection<-	HyperGParams-class
testDirection<-,HyperGParams-method	HyperGParams-class
testDirection<-,LinearMParams-method	LinearMParams-class
testName	HyperGResult-accessors
testName,HyperGResultBase-method	HyperGResult-accessors
testName,LinearMResultBase-method	LinearMResultBase-class
topdown_tree_visitor	tree_visitor
treeLevels	ChrBandTree-class
treeLevels,ChrBandTree-method	ChrBandTree-class
tree_visitor	tree_visitor
ttperm	ttperm
universeBuilder	universeBuilder
universeBuilder,GOHyperGParams-method	universeBuilder
universeBuilder,KEGGHyperGParams-method	universeBuilder
universeBuilder,OBOHyperGParams-method	universeBuilder
universeBuilder,PFAMHyperGParams-method	universeBuilder
universeCounts	HyperGResult-accessors
universeCounts,HyperGResultBase-method	HyperGResult-accessors
universeCounts,LinearMResultBase-method	LinearMResultBase-class
universeGeneIds	HyperGParams-class
universeGeneIds,HyperGParams-method	HyperGParams-class
universeGeneIds,LinearMParams-method	LinearMParams-class
universeMappedCount	HyperGResult-accessors
universeMappedCount,HyperGResultBase-method	HyperGResult-accessors
universeMappedCount,LinearMResultBase-method	LinearMResultBase-class
YeastDatPkg-class	DatPkg-class
