bhklab/CoreGx
Classes and Functions to Serve as the Basis for Other 'Gx' Packages

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bhklab/CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages
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API for bhklab/CoreGx
Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Global functions
$ Man page
$,LongTable-method Man page
$.immutable Man page
$<- Man page
$<-,LongTable-method Man page
$<-.immubtale, Man page
$<-.immutable Man page
. Man page
.CoreSet Man page
.DataMapper Man page
.LongTable Man page
.LongTableDataMapper Man page
.S4MethodContext Source code
.TREDataMapper Man page
.TreatmentResponseExperiment Man page
.all_equals Source code
.assayToBumpyMatrix Man page
.cauchy_loss Source code
.checkForIdColumn Source code
.checkForSampleId Source code
.checkForTreatmentId Source code
.checkMolecularProfiles Source code
.checkTreatmentResponse Source code
.collapse Source code
.combineTest Source code
.convertCSetMolecularProfilesToSE Man page Source code
.corWeighted Source code
.distancePointLine Man page Source code
.distancePointSegment Man page Source code
.dmedncauchys Source code
.dmednnormals Source code
.docs_CoreGx_aggregate Source code
.docs_CoreSet2_constructor Source code
.docs_CoreSet_accessors Source code
.docs_CoreSet_get_annotation Source code
.docs_CoreSet_get_curation Source code
.docs_CoreSet_get_datasetType Source code
.docs_CoreSet_get_dateCreated Source code
.docs_CoreSet_get_fNames Source code
.docs_CoreSet_get_featureInfo Source code
.docs_CoreSet_get_mDataNames Source code
.docs_CoreSet_get_molecularProfiles Source code
.docs_CoreSet_get_molecularProfilesSlot Source code
.docs_CoreSet_get_name Source code
.docs_CoreSet_get_phenoInfo Source code
.docs_CoreSet_get_sampleInfo Source code
.docs_CoreSet_get_sampleNames Source code
.docs_CoreSet_get_sensitivityInfo Source code
.docs_CoreSet_get_treatmentInfo Source code
.docs_CoreSet_get_treatmentNames Source code
.docs_CoreSet_set_annotation Source code
.docs_CoreSet_set_curation Source code
.docs_CoreSet_set_datasetType Source code
.docs_CoreSet_set_dateCreated Source code
.docs_CoreSet_set_fNames Source code
.docs_CoreSet_set_featureInfo Source code
.docs_CoreSet_set_mDataNames Source code
.docs_CoreSet_set_molecularProfiles Source code
.docs_CoreSet_set_molecularProfilesSlot Source code
.docs_CoreSet_set_name Source code
.docs_CoreSet_set_phenoInfo Source code
.docs_CoreSet_set_sampleInfo Source code
.docs_CoreSet_set_sampleNames Source code
.docs_CoreSet_set_treatmentInfo Source code
.docs_CoreSet_set_treatmentNames Source code
.docs_CoreSet_subsetByFeature Source code
.docs_CoreSet_subsetBySample Source code
.docs_CoreSet_subsetByTreatment Source code
.docs_CoreSet_utils Source code
.docs_DataMapper_accessors Source code
.docs_DataMapper_get_rawdata Source code
.docs_DataMapper_set_rawdata Source code
.docs_LongTableDataMapper_get_assayMap Source code
.docs_LongTableDataMapper_get_dimDataMap Source code
.docs_LongTableDataMapper_get_metadataMap Source code
.docs_LongTableDataMapper_set_assayMap Source code
.docs_LongTableDataMapper_set_dimDataMap Source code
.docs_LongTableDataMapper_set_metadataMap Source code
.docs_LongTable_accessors Source code
.edmedncauchys Source code
.edmednnormals Source code
.error Source code
.errorMsg Source code
.examineGOF Source code
.fitCurve Source code
.fitCurve2 Man page Source code
.formatMessage Source code
.freadNA Source code
.funContext Source code
.getExecutionContext Source code
.getSupportVec Source code
.get_dimData Source code
.get_dimDataFromMap Source code
.infoMsg Source code
.intersectList Man page Source code
.length_unique Source code
.linInd Source code
.list_unique Source code
.longTableToSummarizedExperiment Man page
.magnitude Source code
.matInd Source code
.mcc Source code
.merge_longtable_assays Source code
.meshEval Source code
.meshEval2 Source code
.message Source code
.metaConstruct Source code
.multinom Source code
.normal_loss Source code
.parseToRoxygen Source code
.paste_ Source code
.paste_colon Source code
.paste_slashes Source code
.patternSearch Source code
.patternSearch2 Source code
.pmedncauchys Source code
.pmednnormals Source code
.rebuildInfo Source code
.reformatData Source code
.residual Source code
.rmedncauchys Source code
.rmednnormals Source code
.sampling_loss Source code
.sanitizeInput Source code
.selectDataTable Source code
.sensitivityToTRE Source code
.stripWhiteSpace Source code
.subsetByIndex Source code
.subsetMolecularProfilesBySample Source code
.subsetSensitivityBySample Source code
.subsetSensitivityByTreatment Source code
.summarizeMolecularNumbers Source code
.summarizePerturbationNumbers Source code
.summarizeSensitivityNumbers Source code
.symSetDiffList Man page Source code
.table_is_subset Source code
.unionList Man page Source code
.update_dimData Source code
.warnMsg Source code
.warning Source code
CoreGx-defunct Man page
CoreGx-deprecated Man page
CoreSet Man page Source code
CoreSet-accessors Man page
CoreSet-class Man page
CoreSet-utils Man page
CoreSet2 Man page Source code
DataMapper-accessors Man page
DataMapper-class Man page
FUN Source code
LongTable Man page Source code
LongTable-accessors Man page
LongTable-class Man page
LongTableDataMapper Man page Source code
LongTableDataMapper-accessors Man page
LongTableDataMapper-class Man page
Ops.immutable Source code
TREDataMapper Man page Source code
TREDataMapper-accessors Man page
TREDataMapper-class Man page
TreatmentResponseExperiment Man page Source code
TreatmentResponseExperiment-class Man page
[ Man page
[,LongTable,ANY,ANY,ANY-method Man page
[.immutable Man page
[.immutable, Man page
[<- Man page
[<-.immutable Man page
[<-.immutable, Man page
[[ Man page
[[,LongTable,ANY,ANY-method Man page
[[.immutable Man page
[[.immutable, Man page
[[<- Man page
[[<-,LongTable,ANY,ANY-method Man page
[[<-.immutable Man page
[[<-.immutable, Man page
`$.immutable` Source code
`$<-.immutable` Source code
`[.immutable` Source code
`[<-.immutable` Source code
`[[.immutable` Source code
`[[<-.immutable` Source code
`cellInfo<-` Source code
`cellNames<-` Source code
`colnames<-.immutable` Source code
`dimnames<-.immutable` Source code
`names<-.immutable` Source code
`rownames<-.immutable` Source code
`subset<-.immutable` Source code
aggregate,LongTable-method Man page
aggregate,data.table-method Man page
aggregate2 Man page Source code
amcc Man page Source code
annotation Man page
annotation,CoreSet-method Man page
annotation<- Man page
annotation<-,CoreSet,list-method Man page
as Man page
as.long.table Man page Source code
assay,LongTable,ANY-method Man page
assay,LongTableDataMapper,ANY-method Man page
assay,TREDataMapper,ANY-method Man page
assay<-,LongTable,ANY-method Man page
assayCols Man page
assayCols,LongTable-method Man page
assayIndex Man page
assayIndex,LongTable-method Man page
assayKeys Man page
assayKeys,LongTable-method Man page
assayMap Man page
assayMap,LongTableDataMapper,List-method Man page
assayMap,LongTableDataMapper,list-method Man page
assayMap,LongTableDataMapper-method Man page
assayMap,TREDataMapper,List-method Man page
assayMap,TREDataMapper,list-method Man page
assayMap,TREDataMapper-method Man page
assayMap<- Man page
assayMap<-,LongTableDataMapper,List-methhod Man page
assayMap<-,LongTableDataMapper,list-method Man page
assayMap<-,LongTableDataMapper,list_OR_List-method Man page
assayMap<-,TREDataMapper,List-methhod Man page
assayMap<-,TREDataMapper,list-method Man page
assayMap<-,TREDataMapper,list_OR_List-method Man page
assayNames,LongTable-method Man page
assays,LongTable-method Man page
assays,LongTableDataMapper-method Man page
assays,TREDataMapper-method Man page
assays<-,LongTable,list-method Man page
assignment-immutable Man page
buildComboProfiles Man page
buildComboProfiles,LongTable-method Man page
buildLongTable Man page
buildLongTable,character-method Man page
buildLongTable,data.frame-method Man page
buildLongTable,list-method Man page
c.immutable Man page Source code
callingWaterfall Man page Source code
cardinality Man page
cellInfo Man page Source code
cellInfo,CoreSet-method Man page
cellInfo<- Man page
cellInfo<-,CoreSet,data.frame-method Man page
cellName,CoreSet-method Man page
cellNames Man page Source code
cellNames<- Man page
cellNames<-,CoreSet,list-method Man page
checkColumnCardinality Man page Source code
checkCsetStructure Man page Source code
clevelandSmall_cSet Man page
colData,LongTable-method Man page
colData,LongTableDataMapper-method Man page
colData,TREDataMapper-method Man page
colData<-,LongTable,ANY-method Man page
colDataMap Man page
colDataMap,LongTableDataMapper-method Man page
colDataMap,TREDataMapper-method Man page
colDataMap<- Man page
colDataMap<-,LongTableDataMapper,list_OR_List-method Man page
colDataMap<-,TREDataMapper,list_OR_List-method Man page
colDataMap<-LongTableDataMapper,List-method Man page
colDataMap<-TREDataMapper,List-method Man page
colIDs Man page
colIDs,LongTable-method Man page
colMeta Man page
colMeta,LongTable-method Man page
collect_fn_params Man page Source code
colnames,LongTable-method Man page
colnames<- Man page
colnames<-.immutable Man page
colnames<-.immutable, Man page
connectivityScore Man page Source code
cosinePerm Man page Source code
curation Man page
curation,CoreSet-method Man page
curation<- Man page
curation<-,CoreSet,list-method Man page
datasetType Man page
datasetType,CoreSet-method Man page
datasetType<- Man page
datasetType<-,CoreSet,character-method Man page
dateCreated Man page
dateCreated,CoreSet-method Man page
dateCreated<- Man page
dateCreated<-,CoreSet,character-method Man page
dateCreated<-,CoreSet-method Man page
def Source code Source code
dim,LongTable-method Man page
dimnames,LongTable-method Man page
dimnames<- Man page
dimnames<-.immutable Man page
dimnames<-.immutable, Man page
drop_fn_params Man page Source code
drugSensitivitySig Man page
endoaggregate Man page
endoaggregate,LongTable-method Man page
error Source code
exampleDataMapper Man page
fNames Man page
fNames,CoreSet,character-method Man page
fNames<- Man page
fNames<-,CoreSet,character,character-method Man page
featureInfo Man page
featureInfo,CoreSet-method Man page
featureInfo<- Man page
featureInfo<-,CoreSet,character,DataFrame-method Man page
featureInfo<-,CoreSet,character,data.frame-method Man page
getIntern Man page
getIntern,LongTable,character-method Man page
getIntern,LongTable,missing-method Man page
getIntern<- Man page
getIntern<-,LongTable,immutable_list-method Man page
guessMapping Man page
guessMapping,LongTableDataMapper-method Man page
gwc Man page Source code
idCols Man page
idCols,LongTable-method Man page
immutable Man page Source code
immutable_list-class Man page
is.immutable Man page Source code
is.items Man page Source code
is_optim_compatible Man page Source code
lapply,MultiAssayExperiment-method Man page
list_OR_LongTable-class Man page
mDataNames Man page
mDataNames,CoreSet-method Man page
mDataNames<- Man page
mDataNames<-,CoreSet,ANY-method Man page
mDataNames<-,CoreSet-method Man page
make_optim_function Man page Source code
mcc Man page Source code
merckLongTable Man page
mergeAssays Man page
mergeAssays,LongTable-method Man page
metaConstruct Man page
metaConstruct,LongTableDataMapper-method Man page
metaConstruct,TREDataMapper-method Man page
metadata,LongTable-method Man page
metadata<-,LongTable-method Man page
metadataMap Man page
metadataMap,LongTableDataMapper-method Man page
metadataMap,TREDataMapper-method Man page
metadataMap<- Man page
metadataMap<-,LongTableDataMapper,list_OR_List-method Man page
metadataMap<-,LongTableDataMapper-method Man page
metadataMap<-,TREDataMapper,list_OR_List-method Man page
metadataMap<-,TREDataMapper-method Man page
molecularProfiles Man page
molecularProfiles,CoreSet-method Man page
molecularProfiles<- Man page
molecularProfiles<-,CoreSet,character,character,matrix-method Man page
molecularProfiles<-,CoreSet,character,missing,matrix-method Man page
molecularProfiles<-,CoreSet,missing,missing,MutliAssayExperiment Man page
molecularProfiles<-,CoreSet,missing,missing,list-method Man page
molecularProfiles<-,CoreSet,missing,missing,list_OR_MAE-method Man page
molecularProfilesSlot Man page
molecularProfilesSlot,CoreSet-method Man page
molecularProfilesSlot<- Man page
molecularProfilesSlot<-,CoreSet,list-method Man page
molecularProfilesSlot<-,CoreSet,list_OR_MAE-method Man page
molecularProfilesSlot<-CoreSet,MultiAssayExperiment-method Man page
moleculerProfilesSlot,CoreSet-method Man page
mutable Man page Source code
mutable.default Source code
name Man page
name,CoreSet-method Man page
name<- Man page
name<-,CoreSet,character-method Man page
name<-,CoreSet-method Man page
names Man page
names,LongTable-method Man page
names<- Man page
names<-.immutable Man page
nci_TRE_small Man page
optimizeCoreGx Man page Source code
pertNumber Man page
pertNumber,CoreSet-method Man page
pertNumber<- Man page
pertNumber<-,CoreSet,array-method Man page
phenoInfo Man page
phenoInfo,CoreSet,character-method Man page
phenoInfo<- Man page
phenoInfo<-,CoreSet,character,DataFrame-method Man page
phenoInfo<-,CoreSet,character,data.frame-method Man page
print.immutable Man page Source code
printSlot Man page Source code
rawdata Man page
rawdata,DataMapper-method Man page
rawdata,LongTableDataMapper-method Man page
rawdata,TREDataMapper-method Man page
rawdata<- Man page
rawdata<-,DataMapper,ANY-method Man page
rawdata<-,LongTableDataMapper,list-method Man page
rawdata<-,TREDataMapper,list-method Man page
reindex Man page
reindex,LongTable-method Man page
rowData,LongTable-method Man page
rowData,LongTableDataMapper-method Man page
rowData,TREDataMapper-method Man page
rowData<-,LongTable-method Man page
rowDataMap Man page
rowDataMap,LongTableDataMapper-method Man page
rowDataMap,TREDataMapper-method Man page
rowDataMap<- Man page
rowDataMap<-,LongTableDataMapper,list-method Man page
rowDataMap<-,LongTableDataMapper,list_OR_List-method Man page
rowDataMap<-,TREDataMapper,list-method Man page
rowDataMap<-,TREDataMapper,list_OR_List-method Man page
rowDataMap<-LongTableDataMapper,List-method Man page
rowDataMap<-TREDataMapper,List-method Man page
rowIDs Man page
rowIDs,LongTable-method Man page
rowMeta Man page
rowMeta,LongTable-method Man page
rownames,LongTable-method Man page
rownames<- Man page
rownames<-.immutable Man page
rownames<-.immutable, Man page
sampleInfo Man page
sampleInfo,CoreSet-method Man page
sampleInfo<- Man page
sampleInfo<-,CoreSet,data.frame-method Man page
sampleName,CoreSet-method Man page
sampleNames Man page
sampleNames,CoreSet-method Man page
sampleNames<- Man page
sampleNames<-,CoreSet,character-method Man page
sampleNames<-,CoreSet,list-method Man page
sensNumber Man page
sensNumber,CoreSet-method Man page
sensNumber<- Man page
sensNumber<-,CoreSet,matrix-method Man page
sensitivityInfo Man page
sensitivityInfo,CoreSet,character-method Man page
sensitivityInfo,CoreSet,missing-method Man page
sensitivityInfo,CoreSet-method Man page
sensitivityInfo<- Man page
sensitivityInfo<-,CoreSet,data.frame-method Man page
sensitivityInfo<-,CoreSet,missing,data.frame-method Man page
sensitivityMeasures Man page
sensitivityMeasures,CoreSet-method Man page
sensitivityMeasures<- Man page
sensitivityMeasures<-,CoreSet,character-method Man page
sensitivityProfiles Man page
sensitivityProfiles,CoreSet-method Man page
sensitivityProfiles<- Man page
sensitivityProfiles<-,CoreSet,data.frame-method Man page
sensitivityRaw Man page
sensitivityRaw,CoreSet-method Man page
sensitivityRaw<- Man page
sensitivityRaw<-,CoreSet,array-method Man page
sensitivitySlot Man page
sensitivitySlot<- Man page
sensitivitySlotToLongTable Man page
sensitvityInfo<-,CoreSet,character,data.frame-method Man page
setOps-immutable Man page
show,CoreSet-method Man page
show,LongTable-method Man page
show,LongTableDataMapper-method Man page
show.immutable Man page Source code
showSigAnnot Man page
subset, Man page
subset,LongTable-method Man page
subset.immutable Man page Source code
subset<-.immutable Man page
subset<-.immutable, Man page
subsetByFeature Man page
subsetByFeature,CoreSet-method Man page
subsetBySample Man page
subsetBySample,CoreSet-method Man page
subsetByTreatment Man page
subsetByTreatment,CoreSet-method Man page
subsetTo Man page
summarizeMolecularProfiles Man page
summarizeSensitivityProfiles Man page
treamentResponse<-,CoreSet,list-method Man page
treatmentInfo Man page
treatmentInfo,CoreSet-method Man page
treatmentInfo<- Man page
treatmentInfo<-,CoreSet,data.frame-method Man page
treatmentNames Man page
treatmentNames,CoreSet-method Man page
treatmentNames<- Man page
treatmentNames<-,CoreSet,character-method Man page
treatmentResponse Man page
treatmentResponse,CoreSet-method Man page
treatmentResponse<- Man page
treatmentResponse<-,CoreSet,LongTable-method Man page
treatmentResponse<-,CoreSet,list_OR_LongTable-method Man page
updateObject,CoreSet-method Man page
updateObject,LongTable-method Man page
updateSampleId Man page Source code
updateTreatmentId Man page Source code
bhklab/CoreGx documentation built on March 14, 2024, 3:04 a.m.

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