Files in bhklab/CoreGx

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

CODE_OF_CONDUCT.md CONTRIBUTING.md LICENSE.md NEWS.md R/CoreSet-accessors.R R/CoreSet-class.R R/CoreSet-utils.R R/DataMapper-class.R R/LongTable-accessors.R R/LongTable-class.R R/LongTable-utils.R R/LongTableDataMapper-accessors.R R/LongTableDataMapper-class.R R/TREDataMapper-class.R R/TreatmentResponseExperiment-class.R R/adaptiveMatthewCor.R R/aggregate-methods.R R/allGenerics.R R/callingWaterfall.R R/connectivityScore.R R/cosinePerm.R R/datasets.R R/deprecated.R R/endoaggregate-methods.R R/globals.R R/gwc.R R/immutable-class.R R/matthewCor.R R/mergeAssays-method.R R/methods-coerce.R R/methods-dim.R R/methods-dimnames.R R/methods-drugSensitivitySig.R R/methods-guessMapping.R R/methods-metaConstruct.R R/methods-subsetTo.R R/optimizeCoreGx.R R/updateObject-methods.R R/utilities.R R/utils-iteration.R R/utils-messages.R R/utils-optimization.R R/utils-testing.R R/utils-updateS4.R README.md man/CoreGx-deprecated.Rd man/CoreSet-accessors.Rd man/CoreSet-class.Rd man/CoreSet-utils.Rd man/CoreSet.Rd man/CoreSet2.Rd man/DataMapper-accessors.Rd man/DataMapper-class.Rd man/LongTable-accessors.Rd man/LongTable-class.Rd man/LongTable.Rd man/LongTableDataMapper-accessors.Rd man/LongTableDataMapper-class.Rd man/LongTableDataMapper.Rd man/TREDataMapper-accessors.Rd man/TREDataMapper-class.Rd man/TREDataMapper.Rd man/TreatmentResponseExperiment-class.Rd man/TreatmentResponseExperiment.Rd man/aggregate-LongTable-method.Rd man/aggregate-data.table-method.Rd man/aggregate2.Rd man/amcc.Rd man/as.Rd man/as.long.table.Rd man/assay-LongTableDataMapper-ANY-method.Rd man/assay-TREDataMapper-ANY-method.Rd man/assayCols.Rd man/assayIndex.Rd man/assayKeys.Rd man/assays-LongTableDataMapper-method.Rd man/assays-TREDataMapper-method.Rd man/assignment-immutable.Rd man/buildComboProfiles-LongTable-method.Rd man/buildComboProfiles.Rd man/buildLongTable-character-method.Rd man/buildLongTable-data.frame-method.Rd man/buildLongTable-list-method.Rd man/buildLongTable.Rd man/c.immutable.Rd man/callingWaterfall.Rd man/cash-LongTable-method.Rd man/cash-set-LongTable-method.Rd man/checkColumnCardinality.Rd man/checkCsetStructure.Rd man/clevelandSmall_cSet.Rd man/colData-LongTableDataMapper-method.Rd man/colData-TREDataMapper-method.Rd man/colIDs.Rd man/colMeta.Rd man/collect_fn_params.Rd man/connectivityScore.Rd man/cosinePerm.Rd man/dot-.Rd man/dot-assayToBumpyMatrix.Rd man/dot-convertCSetMolecularProfilesToSE.Rd man/dot-distancePointLine.Rd man/dot-distancePointSegment.Rd man/dot-fitCurve2.Rd man/dot-intersectList.Rd man/dot-longTableToSummarizedExperiment.Rd man/dot-symSetDiffList.Rd man/dot-unionList.Rd man/drop_fn_params.Rd man/drugSensitivitySig.Rd man/endoaggregate-LongTable-method.Rd man/endoaggregate.Rd man/exampleDataMapper.Rd man/getIntern-set-LongTable-immutable_list-method.Rd man/getIntern-set.Rd man/getIntern.Rd man/guessMapping-LongTableDataMapper-method.Rd man/guessMapping.Rd man/gwc.Rd man/idCols.Rd man/immutable.Rd man/is.items.Rd man/is_optim_compatible.Rd man/lapply-MultiAssayExperiment-method.Rd man/list_OR_LongTable-class.Rd man/make_optim_function.Rd man/mcc.Rd man/merckLongTable.Rd man/mergeAssays-LongTable-method.Rd man/mergeAssays.Rd man/metaConstruct.Rd man/metadata-LongTable-method.Rd man/metadata-set-LongTable-method.Rd man/mutable.Rd man/nci_TRE_small.Rd man/optimizeCoreGx.Rd man/printSlot.Rd man/reindex-LongTable-method.Rd man/reindex.Rd man/rowData-LongTableDataMapper-method.Rd man/rowData-TREDataMapper-method.Rd man/rowIDs.Rd man/rowMeta.Rd man/sensitivityInfo-set.Rd man/sensitivityInfo.Rd man/sensitivityMeasures-set.Rd man/sensitivityMeasures.Rd man/sensitivityProfiles-set.Rd man/sensitivityProfiles.Rd man/sensitivityRaw-set.Rd man/sensitivityRaw.Rd man/sensitivitySlotToLongTable.Rd man/setOps-immutable.Rd man/show-CoreSet-method.Rd man/show-LongTable-method.Rd man/showSigAnnot.Rd man/sub-LongTable-ANY-ANY-ANY-method.Rd man/sub-subset-LongTable-ANY-ANY-method.Rd man/subset-LongTable-method.Rd man/subsetTo.Rd man/summarizeMolecularProfiles.Rd man/summarizeSensitivityProfiles.Rd man/updateObject-CoreSet-method.Rd man/updateObject-LongTable-method.Rd man/updateSampleId.Rd man/updateTreatmentId.Rd tests/testthat.R tests/testthat/test-LongTable-accessors.R tests/testthat/test-LongTable-class.R tests/testthat/test-LongTable-utils.R tests/testthat/test-aggregate-methods.R tests/testthat/test-utils-optimization.R vignettes/TreatmentResponseExperiment.Rmd vignettes/coreGx.Rmd