PCpheno-package	PCpheno.package
annotation,HyperGParams-method	CoHyperGParams-class
buildFDMat	buildFDMat
categoryName	CoHyperGParams-class
categoryName,HyperGParams-method	CoHyperGParams-class
categoryToEntrezBuilder	categoryToEntrezBuilder
categoryToEntrezBuilder,CoHyperGParams-method	categoryToEntrezBuilder
CoHyperGParams-class	CoHyperGParams-class
CoHyperGResult-class	CoHyperGResult-class
complexStatus	complexStatus
conditional	CoHyperGParams-class
conditional,HyperGParams-method	CoHyperGParams-class
conditional<-	CoHyperGParams-class
densityEstimate	densityEstimate
deResult-class	deResult-class
Dudley	Dudley
DudleyGenelist	Dudley
DudleyPhenoFull	Dudley
DudleyPhenoM	Dudley
Dudleyresult	Dudley
DudleySign	Dudley
expectedCounts,CoHyperGResult-method	CoHyperGResult-class
geneCounts,CoHyperGResult-method	CoHyperGResult-class
geneIds,HyperGParams-method	CoHyperGParams-class
geneIds<-	CoHyperGParams-class
geneIds<-,HyperGParams,logical-method	CoHyperGParams-class
geneIds<-,HyperGParams-method	CoHyperGParams-class
getDescr	getDescr
getFDgene	getFDgene
GiaeverExpCdt	Giaever
GiaeverGene	Giaever
GiaeverPheno	Giaever
Giaeverresult	Giaever
graphTheory	graphTheory
gtResult-class	gtResult-class
HI	HI
HyperGParams-class	CoHyperGParams-class
hyperGTest,CoHyperGParams-method	CoHyperGParams-class
isConditional	CoHyperGParams-class
isConditional,HyperGParams-method	CoHyperGParams-class
KastenmayerRaw	Kastenmayer
KEGG2SCISI	KEGG2SCISI
LesageRaw	Lesage
oddsRatios,CoHyperGResult-method	CoHyperGResult-class
ontology	CoHyperGParams-class
ontology,HyperGParams-method	CoHyperGParams-class
ontology<-	CoHyperGParams-class
OsterbergRaw	Osterberg
overlap	overlap
PCpheno	PCpheno.package
plot	plot
plot,deResult,missing-method	plot
plot,deResult-method	plot
plot,gtResult,missing-method	plot
plot,gtResult-method	plot
ppiInteract	ppiInteraction
pvalueCutoff,HyperGParams-method	CoHyperGParams-class
pvalueCutoff<-	CoHyperGParams-class
pvalueCutoff<-,HyperGParams-method	CoHyperGParams-class
pvalues,CoHyperGResult-method	CoHyperGResult-class
reduceM	reduceM
SGDphenoL	SGDphenoL
summary,CoHyperGResult-method	CoHyperGResult-class
testDirection,HyperGParams-method	CoHyperGParams-class
testDirection<-	CoHyperGParams-class
testDirection<-,HyperGParams-method	CoHyperGParams-class
testResult-class	testResult-class
truncName	truncName
universeBuilder,CoHyperGParams-method	CoHyperGParams-class
universeCounts,CoHyperGResult-method	CoHyperGResult-class
universeGeneIds	CoHyperGParams-class
universeGeneIds,HyperGParams-method	CoHyperGParams-class
YEASTOHNOLOG	YEASTOHNOLOG
