$	setOps-immutable
$,LongTable-method	cash-LongTable-method
$.immutable	setOps-immutable
$<-	assignment-immutable
$<-,LongTable-method	cash-set-LongTable-method
$<-.immubtale,	assignment-immutable
$<-.immutable	assignment-immutable
.	dot-
.assayToBumpyMatrix	dot-assayToBumpyMatrix
.convertCSetMolecularProfilesToSE	dot-convertCSetMolecularProfilesToSE
.CoreSet	CoreSet-class
.DataMapper	DataMapper-class
.distancePointLine	dot-distancePointLine
.distancePointSegment	dot-distancePointSegment
.fitCurve2	dot-fitCurve2
.intersectList	dot-intersectList
.LongTable	LongTable-class
.LongTableDataMapper	LongTableDataMapper-class
.longTableToSummarizedExperiment	dot-longTableToSummarizedExperiment
.symSetDiffList	dot-symSetDiffList
.TreatmentResponseExperiment	TreatmentResponseExperiment-class
.TREDataMapper	TREDataMapper-class
.unionList	dot-unionList
aggregate,data.table-method	aggregate-data.table-method
aggregate,LongTable-method	aggregate-LongTable-method
aggregate2	aggregate2
amcc	amcc
annotation	CoreSet-accessors
annotation,CoreSet-method	CoreSet-accessors
annotation<-	CoreSet-accessors
annotation<-,CoreSet,list-method	CoreSet-accessors
as	as
as.long.table	as.long.table
assay,LongTable,ANY-method	LongTable-class
assay,LongTableDataMapper,ANY-method	assay-LongTableDataMapper-ANY-method
assay,TREDataMapper,ANY-method	assay-TREDataMapper-ANY-method
assay<-,LongTable,ANY-method	LongTable-class
assayCols	assayCols
assayCols,LongTable-method	LongTable-class
assayIndex	assayIndex
assayIndex,LongTable-method	LongTable-class
assayKeys	assayKeys
assayKeys,LongTable-method	LongTable-class
assayMap	TREDataMapper-accessors
assayMap,LongTableDataMapper,List-method	LongTableDataMapper-accessors
assayMap,LongTableDataMapper,list-method	LongTableDataMapper-accessors
assayMap,LongTableDataMapper-method	LongTableDataMapper-accessors
assayMap,TREDataMapper,List-method	TREDataMapper-accessors
assayMap,TREDataMapper,list-method	TREDataMapper-accessors
assayMap,TREDataMapper-method	TREDataMapper-accessors
assayMap<-	TREDataMapper-accessors
assayMap<-,LongTableDataMapper,List-methhod	LongTableDataMapper-accessors
assayMap<-,LongTableDataMapper,list-method	LongTableDataMapper-accessors
assayMap<-,LongTableDataMapper,list_OR_List-method	LongTableDataMapper-accessors
assayMap<-,TREDataMapper,List-methhod	TREDataMapper-accessors
assayMap<-,TREDataMapper,list-method	TREDataMapper-accessors
assayMap<-,TREDataMapper,list_OR_List-method	TREDataMapper-accessors
assayNames,LongTable-method	LongTable-class
assays,LongTable-method	LongTable-class
assays,LongTableDataMapper-method	assays-LongTableDataMapper-method
assays,TREDataMapper-method	assays-TREDataMapper-method
assays<-,LongTable,list-method	LongTable-class
assignment-immutable	assignment-immutable
buildComboProfiles	buildComboProfiles
buildComboProfiles,LongTable-method	buildComboProfiles-LongTable-method
buildLongTable	buildLongTable
buildLongTable,character-method	buildLongTable-character-method
buildLongTable,data.frame-method	buildLongTable-data.frame-method
buildLongTable,list-method	buildLongTable-list-method
c.immutable	c.immutable
callingWaterfall	callingWaterfall
cardinality	checkColumnCardinality
cellInfo	CoreSet-accessors
cellInfo,CoreSet-method	CoreSet-accessors
cellInfo<-	CoreSet-accessors
cellInfo<-,CoreSet,data.frame-method	CoreSet-accessors
cellName,CoreSet-method	CoreSet-accessors
cellNames	CoreSet-accessors
cellNames<-	CoreSet-accessors
cellNames<-,CoreSet,list-method	CoreSet-accessors
checkColumnCardinality	checkColumnCardinality
checkCsetStructure	checkCsetStructure
clevelandSmall_cSet	clevelandSmall_cSet
colData,LongTable-method	LongTable-class
colData,LongTableDataMapper-method	colData-LongTableDataMapper-method
colData,TREDataMapper-method	colData-TREDataMapper-method
colData<-,LongTable,ANY-method	LongTable-class
colDataMap	TREDataMapper-accessors
colDataMap,LongTableDataMapper-method	LongTableDataMapper-accessors
colDataMap,TREDataMapper-method	TREDataMapper-accessors
colDataMap<-	TREDataMapper-accessors
colDataMap<-,LongTableDataMapper,list_OR_List-method	LongTableDataMapper-accessors
colDataMap<-,TREDataMapper,list_OR_List-method	TREDataMapper-accessors
colDataMap<-LongTableDataMapper,List-method	LongTableDataMapper-accessors
colDataMap<-TREDataMapper,List-method	TREDataMapper-accessors
colIDs	colIDs
colIDs,LongTable-method	LongTable-class
collect_fn_params	collect_fn_params
colMeta	colMeta
colMeta,LongTable-method	LongTable-class
colnames,LongTable-method	LongTable-class
colnames<-	assignment-immutable
colnames<-.immutable	assignment-immutable
colnames<-.immutable,	assignment-immutable
connectivityScore	connectivityScore
CoreGx-defunct	CoreGx-deprecated
CoreGx-deprecated	CoreGx-deprecated
CoreSet	CoreSet
CoreSet-accessors	CoreSet-accessors
CoreSet-class	CoreSet-class
CoreSet-utils	CoreSet-utils
CoreSet2	CoreSet2
cosinePerm	cosinePerm
curation	CoreSet-accessors
curation,CoreSet-method	CoreSet-accessors
curation<-	CoreSet-accessors
curation<-,CoreSet,list-method	CoreSet-accessors
DataMapper-accessors	DataMapper-accessors
DataMapper-class	DataMapper-class
datasetType	CoreSet-accessors
datasetType,CoreSet-method	CoreSet-accessors
datasetType<-	CoreSet-accessors
datasetType<-,CoreSet,character-method	CoreSet-accessors
dateCreated	CoreSet-accessors
dateCreated,CoreSet-method	CoreSet-accessors
dateCreated<-	CoreSet-accessors
dateCreated<-,CoreSet,character-method	CoreSet-accessors
dateCreated<-,CoreSet-method	CoreSet-accessors
dim,LongTable-method	LongTable-class
dimnames,LongTable-method	LongTable-class
dimnames<-	assignment-immutable
dimnames<-.immutable	assignment-immutable
dimnames<-.immutable,	assignment-immutable
drop_fn_params	drop_fn_params
drugSensitivitySig	drugSensitivitySig
endoaggregate	endoaggregate
endoaggregate,LongTable-method	endoaggregate-LongTable-method
exampleDataMapper	exampleDataMapper
featureInfo	CoreSet-accessors
featureInfo,CoreSet-method	CoreSet-accessors
featureInfo<-	CoreSet-accessors
featureInfo<-,CoreSet,character,data.frame-method	CoreSet-accessors
featureInfo<-,CoreSet,character,DataFrame-method	CoreSet-accessors
fNames	CoreSet-accessors
fNames,CoreSet,character-method	CoreSet-accessors
fNames<-	CoreSet-accessors
fNames<-,CoreSet,character,character-method	CoreSet-accessors
getIntern	getIntern
getIntern,LongTable,character-method	LongTable-class
getIntern,LongTable,missing-method	LongTable-class
getIntern<-	getIntern-set
getIntern<-,LongTable,immutable_list-method	getIntern-set-LongTable-immutable_list-method
guessMapping	guessMapping
guessMapping,LongTableDataMapper-method	guessMapping-LongTableDataMapper-method
gwc	gwc
idCols	idCols
idCols,LongTable-method	LongTable-class
immutable	immutable
immutable_list-class	immutable
is.immutable	immutable
is.items	is.items
is_optim_compatible	is_optim_compatible
lapply,MultiAssayExperiment-method	lapply-MultiAssayExperiment-method
list_OR_LongTable-class	list_OR_LongTable-class
LongTable	LongTable
LongTable-accessors	LongTable-accessors
LongTable-class	LongTable-class
LongTableDataMapper	LongTableDataMapper
LongTableDataMapper-accessors	LongTableDataMapper-accessors
LongTableDataMapper-class	LongTableDataMapper-class
make_optim_function	make_optim_function
mcc	mcc
mDataNames	CoreSet-accessors
mDataNames,CoreSet-method	CoreSet-accessors
mDataNames<-	CoreSet-accessors
mDataNames<-,CoreSet,ANY-method	CoreSet-accessors
mDataNames<-,CoreSet-method	CoreSet-accessors
merckLongTable	merckLongTable
mergeAssays	mergeAssays
mergeAssays,LongTable-method	mergeAssays-LongTable-method
metaConstruct	metaConstruct
metaConstruct,LongTableDataMapper-method	metaConstruct
metaConstruct,TREDataMapper-method	metaConstruct
metadata,LongTable-method	metadata-LongTable-method
metadata<-,LongTable-method	metadata-set-LongTable-method
metadataMap	TREDataMapper-accessors
metadataMap,LongTableDataMapper-method	LongTableDataMapper-accessors
metadataMap,TREDataMapper-method	TREDataMapper-accessors
metadataMap<-	TREDataMapper-accessors
metadataMap<-,LongTableDataMapper,list_OR_List-method	LongTableDataMapper-accessors
metadataMap<-,LongTableDataMapper-method	LongTableDataMapper-accessors
metadataMap<-,TREDataMapper,list_OR_List-method	TREDataMapper-accessors
metadataMap<-,TREDataMapper-method	TREDataMapper-accessors
molecularProfiles	CoreSet-accessors
molecularProfiles,CoreSet-method	CoreSet-accessors
molecularProfiles<-	CoreSet-accessors
molecularProfiles<-,CoreSet,character,character,matrix-method	CoreSet-accessors
molecularProfiles<-,CoreSet,character,missing,matrix-method	CoreSet-accessors
molecularProfiles<-,CoreSet,missing,missing,list-method	CoreSet-accessors
molecularProfiles<-,CoreSet,missing,missing,list_OR_MAE-method	CoreSet-accessors
molecularProfiles<-,CoreSet,missing,missing,MutliAssayExperiment-method	CoreSet-accessors
molecularProfilesSlot	CoreSet-accessors
molecularProfilesSlot,CoreSet-method	CoreSet-accessors
molecularProfilesSlot<-	CoreSet-accessors
molecularProfilesSlot<-,CoreSet,list-method	CoreSet-accessors
molecularProfilesSlot<-,CoreSet,list_OR_MAE-method	CoreSet-accessors
molecularProfilesSlot<-CoreSet,MultiAssayExperiment-method	CoreSet-accessors
moleculerProfilesSlot,CoreSet-method	CoreSet-accessors
mutable	mutable
name	CoreSet-accessors
name,CoreSet-method	CoreSet-accessors
name<-	CoreSet-accessors
name<-,CoreSet,character-method	CoreSet-accessors
name<-,CoreSet-method	CoreSet-accessors
names	LongTable-class
names,LongTable-method	LongTable-class
names<-	assignment-immutable
names<-.immutable	assignment-immutable
nci_TRE_small	nci_TRE_small
optimizeCoreGx	optimizeCoreGx
pertNumber	CoreSet-accessors
pertNumber,CoreSet-method	CoreSet-accessors
pertNumber<-	CoreSet-accessors
pertNumber<-,CoreSet,array-method	CoreSet-accessors
phenoInfo	CoreSet-accessors
phenoInfo,CoreSet,character-method	CoreSet-accessors
phenoInfo<-	CoreSet-accessors
phenoInfo<-,CoreSet,character,data.frame-method	CoreSet-accessors
phenoInfo<-,CoreSet,character,DataFrame-method	CoreSet-accessors
print.immutable	immutable
rawdata	DataMapper-accessors
rawdata,DataMapper-method	DataMapper-accessors
rawdata,LongTableDataMapper-method	LongTableDataMapper-accessors
rawdata,TREDataMapper-method	TREDataMapper-accessors
rawdata<-	DataMapper-accessors
rawdata<-,DataMapper,ANY-method	DataMapper-accessors
rawdata<-,LongTableDataMapper,list-method	LongTableDataMapper-accessors
rawdata<-,TREDataMapper,list-method	TREDataMapper-accessors
reindex	reindex
reindex,LongTable-method	reindex-LongTable-method
rowData,LongTable-method	LongTable-class
rowData,LongTableDataMapper-method	rowData-LongTableDataMapper-method
rowData,TREDataMapper-method	rowData-TREDataMapper-method
rowData<-,LongTable-method	LongTable-class
rowDataMap	TREDataMapper-accessors
rowDataMap,LongTableDataMapper-method	LongTableDataMapper-accessors
rowDataMap,TREDataMapper-method	TREDataMapper-accessors
rowDataMap<-	TREDataMapper-accessors
rowDataMap<-,LongTableDataMapper,list-method	LongTableDataMapper-accessors
rowDataMap<-,LongTableDataMapper,list_OR_List-method	LongTableDataMapper-accessors
rowDataMap<-,TREDataMapper,list-method	TREDataMapper-accessors
rowDataMap<-,TREDataMapper,list_OR_List-method	TREDataMapper-accessors
rowDataMap<-LongTableDataMapper,List-method	LongTableDataMapper-accessors
rowDataMap<-TREDataMapper,List-method	TREDataMapper-accessors
rowIDs	rowIDs
rowIDs,LongTable-method	LongTable-class
rowMeta	rowMeta
rowMeta,LongTable-method	LongTable-class
rownames,LongTable-method	LongTable-class
rownames<-	assignment-immutable
rownames<-.immutable	assignment-immutable
rownames<-.immutable,	assignment-immutable
sampleInfo	CoreSet-accessors
sampleInfo,CoreSet-method	CoreSet-accessors
sampleInfo<-	CoreSet-accessors
sampleInfo<-,CoreSet,data.frame-method	CoreSet-accessors
sampleName,CoreSet-method	CoreSet-accessors
sampleNames	CoreSet-accessors
sampleNames,CoreSet-method	CoreSet-accessors
sampleNames<-	CoreSet-accessors
sampleNames<-,CoreSet,character-method	CoreSet-accessors
sampleNames<-,CoreSet,list-method	CoreSet-accessors
sensitivityInfo	sensitivityInfo
sensitivityInfo,CoreSet,character-method	CoreSet-accessors
sensitivityInfo,CoreSet,missing-method	CoreSet-accessors
sensitivityInfo,CoreSet-method	CoreSet-accessors
sensitivityInfo<-	sensitivityInfo-set
sensitivityInfo<-,CoreSet,data.frame-method	CoreSet-accessors
sensitivityInfo<-,CoreSet,missing,data.frame-method	CoreSet-accessors
sensitivityMeasures	sensitivityMeasures
sensitivityMeasures,CoreSet-method	CoreSet-accessors
sensitivityMeasures<-	sensitivityMeasures-set
sensitivityMeasures<-,CoreSet,character-method	CoreSet-accessors
sensitivityProfiles	sensitivityProfiles
sensitivityProfiles,CoreSet-method	CoreSet-accessors
sensitivityProfiles<-	sensitivityProfiles-set
sensitivityProfiles<-,CoreSet,data.frame-method	CoreSet-accessors
sensitivityRaw	sensitivityRaw
sensitivityRaw,CoreSet-method	CoreSet-accessors
sensitivityRaw<-	sensitivityRaw-set
sensitivityRaw<-,CoreSet,array-method	CoreSet-accessors
sensitivitySlot	CoreSet-accessors
sensitivitySlot<-	CoreSet-accessors
sensitivitySlotToLongTable	sensitivitySlotToLongTable
sensitvityInfo<-,CoreSet,character,data.frame-method	CoreSet-accessors
sensNumber	CoreSet-accessors
sensNumber,CoreSet-method	CoreSet-accessors
sensNumber<-	CoreSet-accessors
sensNumber<-,CoreSet,matrix-method	CoreSet-accessors
setOps-immutable	setOps-immutable
show,CoreSet-method	show-CoreSet-method
show,LongTable-method	show-LongTable-method
show,LongTableDataMapper-method	LongTableDataMapper-class
show.immutable	immutable
showSigAnnot	showSigAnnot
subset,	setOps-immutable
subset,LongTable-method	subset-LongTable-method
subset.immutable	setOps-immutable
subset<-.immutable	assignment-immutable
subset<-.immutable,	assignment-immutable
subsetByFeature	CoreSet-utils
subsetByFeature,CoreSet-method	CoreSet-utils
subsetBySample	CoreSet-utils
subsetBySample,CoreSet-method	CoreSet-utils
subsetByTreatment	CoreSet-utils
subsetByTreatment,CoreSet-method	CoreSet-utils
subsetTo	subsetTo
summarizeMolecularProfiles	summarizeMolecularProfiles
summarizeSensitivityProfiles	summarizeSensitivityProfiles
treamentResponse<-,CoreSet,list-method	CoreSet-accessors
treatmentInfo	CoreSet-accessors
treatmentInfo,CoreSet-method	CoreSet-accessors
treatmentInfo<-	CoreSet-accessors
treatmentInfo<-,CoreSet,data.frame-method	CoreSet-accessors
treatmentNames	CoreSet-accessors
treatmentNames,CoreSet-method	CoreSet-accessors
treatmentNames<-	CoreSet-accessors
treatmentNames<-,CoreSet,character-method	CoreSet-accessors
treatmentResponse	CoreSet-accessors
treatmentResponse,CoreSet-method	CoreSet-accessors
treatmentResponse<-	CoreSet-accessors
treatmentResponse<-,CoreSet,list_OR_LongTable-method	CoreSet-accessors
treatmentResponse<-,CoreSet,LongTable-method	CoreSet-accessors
TreatmentResponseExperiment	TreatmentResponseExperiment
TreatmentResponseExperiment-class	TreatmentResponseExperiment-class
TREDataMapper	TREDataMapper
TREDataMapper-accessors	TREDataMapper-accessors
TREDataMapper-class	TREDataMapper-class
updateObject,CoreSet-method	updateObject-CoreSet-method
updateObject,LongTable-method	updateObject-LongTable-method
updateSampleId	updateSampleId
updateTreatmentId	updateTreatmentId
[	setOps-immutable
[,LongTable,ANY,ANY,ANY-method	sub-LongTable-ANY-ANY-ANY-method
[.immutable	setOps-immutable
[.immutable,	setOps-immutable
[<-	assignment-immutable
[<-.immutable	assignment-immutable
[<-.immutable,	assignment-immutable
[[	setOps-immutable
[[,LongTable,ANY,ANY-method	LongTable-class
[[.immutable	setOps-immutable
[[.immutable,	setOps-immutable
[[<-	assignment-immutable
[[<-,LongTable,ANY,ANY-method	sub-subset-LongTable-ANY-ANY-method
[[<-.immutable	assignment-immutable
[[<-.immutable,	assignment-immutable
