aespca	aespca
AESPCA_pVals	AESPCA_pVals
AESPCA_pVals,OmicsPathway-method	AESPCA_pVals
CheckAssay	CheckAssay
CheckPwyColl	CheckPwyColl
CheckSampleIDs	CheckSampleIDs
colonSurv_df	colonSurv_df
colon_pathwayCollection	colon_pathwayCollection
Contains	Contains
ControlFDR	ControlFDR
coxTrain_fun	coxTrain_fun
CreateOmics	CreateOmics
CreateOmicsCateg	CreateOmicsPathway
CreateOmicsPath	CreateOmicsPathway
CreateOmicsReg	CreateOmicsPathway
CreateOmicsSurv	CreateOmicsPathway
CreatePathwayCollection	CreatePathwayCollection
ExtractAESPCs	ExtractAESPCs
ExtractAESPCs,OmicsPathway-method	ExtractAESPCs
getAssay	get_set_OmicsPathway
getAssay,OmicsPathway-method	get_set_OmicsPathway
getAssay<-	get_set_OmicsPathway
getAssay<-,OmicsPathway-method	get_set_OmicsPathway
getEvent	get_set_OmicsSurv
getEvent,OmicsSurv-method	get_set_OmicsSurv
getEvent<-	get_set_OmicsSurv
getEvent<-,OmicsSurv-method	get_set_OmicsSurv
getEventTime	get_set_OmicsSurv
getEventTime,OmicsSurv-method	get_set_OmicsSurv
getEventTime<-	get_set_OmicsSurv
getEventTime<-,OmicsSurv-method	get_set_OmicsSurv
getPathPCLs	getPathPCLs
getPathPCLs.aespcOut	getPathPCLs
getPathPCLs.superpcOut	getPathPCLs
getPathpVals	getPathpVals
getPathpVals.aespcOut	getPathpVals
getPathpVals.superpcOut	getPathpVals
getPathwayCollection	get_set_OmicsPathway
getPathwayCollection,OmicsPathway-method	get_set_OmicsPathway
getPathwayCollection<-	get_set_OmicsPathway
getPathwayCollection<-,OmicsPathway-method	get_set_OmicsPathway
getResponse	get_set_OmicsRegCateg
getResponse,OmicsPathway-method	get_set_OmicsRegCateg
getResponse<-	get_set_OmicsRegCateg
getResponse<-,OmicsPathway-method	get_set_OmicsRegCateg
getSampleIDs	get_set_OmicsPathway
getSampleIDs,OmicsPathway-method	get_set_OmicsPathway
getSampleIDs<-	get_set_OmicsPathway
getSampleIDs<-,OmicsPathway-method	get_set_OmicsPathway
getTrimPathwayCollection	get_set_OmicsPathway
getTrimPathwayCollection,OmicsPathway-method	get_set_OmicsPathway
glmTrain_fun	glmTrain_fun
GumbelMixpValues	GumbelMixpValues
IntersectOmicsPwyCollct	IntersectOmicsPwyCollct
IntersectOmicsPwyCollct,OmicsPathway-method	IntersectOmicsPwyCollct
JoinPhenoAssay	JoinPhenoAssay
lars.lsa	lars.lsa
LoadOntoPCs	LoadOntoPCs
mysvd	mysvd
normalize	normalize
olsTrain_fun	olsTrain_fun
OmicsCateg-class	OmicsCateg-class
OmicsPathway-class	OmicsPathway-class
OmicsReg-class	OmicsReg-class
OmicsSurv-class	OmicsSurv-class
OptimGumbelMixParams	OptimGumbelMixParams
pathwayPCA	pathwayPCA-package
PathwaytValues	PathwaytValues
pathway_tControl	pathway_tControl
pathway_tScores	pathway_tScores
PermTestCateg	PermTestCateg
PermTestCateg,OmicsCateg-method	PermTestCateg
PermTestReg	PermTestReg
PermTestReg,OmicsReg-method	PermTestReg
PermTestSurv	PermTestSurv
PermTestSurv,OmicsSurv-method	PermTestSurv
print.pathwayCollection	print.pathwayCollection
RandomControlSample	permuteSamps
read_gmt	read_gmt
SampleCateg	permuteSamps
SampleReg	permuteSamps
SampleResponses	permuteSamps
SampleSurv	permuteSamps
SE2Tidy	SE2Tidy
show,OmicsPathway-method	show-OmicsPathway-method
SubsetOmicsPath	get_set_OmicsPathway
SubsetOmicsResponse	get_set_OmicsRegCateg
SubsetOmicsSurv	get_set_OmicsSurv
SubsetPathwayCollection	SubsetPathwayCollection
SubsetPathwayData	SubsetPathwayData
SubsetPathwayData,OmicsPathway-method	SubsetPathwayData
superpc.st	superpc.st
superpc.train	superpc.train
SuperPCA_pVals	SuperPCA_pVals
SuperPCA_pVals,OmicsPathway-method	SuperPCA_pVals
TabulatepValues	TabulatepValues
TransposeAssay	TransposeAssay
ValidOmicsCateg	ValidOmicsSurv
ValidOmicsReg	ValidOmicsSurv
ValidOmicsSurv	ValidOmicsSurv
WhichPathways	WhichPathways
wikipwsHS_Entrez_pathwayCollection	wikipwsHS_Entrez_pathwayCollection
wikipwsHS_Symbol_pathwayCollection	wikipwsHS_Symbol_pathwayCollection
write_gmt	write_gmt
[[.pathwayCollection	SubsetPathwayCollection
