.                       Convenience function for converting R code to a
                        call
.assayToBumpyMatrix     Convert a LongTable assay into a BumpyMatrix
                        object
.fitCurve2              Curve fitting via 'stats::optim' L-BFGS-B with
                        fall-back grid/pattern search if convergence is
                        not achieved.
.longTableToSummarizedExperiment
                        Convert LongTable to gDR Style
                        SummarizedExperiment
[,LongTable,ANY,ANY,ANY-method
                        [ LongTable Method
[[<-,LongTable,ANY,ANY-method
                        [[<- Method for LongTable Class
$,LongTable-method      Select an assay from a LongTable object
$<-,LongTable-method    Update an assay from a LongTable object
aggregate,data.table-method
                        Functional S4 API for aggregation over a
                        'data.table' object.
aggregate,LongTable-method
                        Functional API for aggregation over a
                        'LongTable' or inheriting class
aggregate2              Functional API for data.table aggregation which
                        allows capture of associated aggregate calls so
                        they can be recomputed later.
amcc                    Calculate an Adaptive Matthews Correlation
                        Coefficient
as                      Coerce a 'LongTable' to a
                        'TreatmentResponseExperiment'
as.long.table           Coerce from data.table to LongTable
assayCols               Generic to access the assay columns of a
                        rectangular object.
assayIndex              Retrieve and assayIndex
assayKeys               Retrieve a set of assayKeys
assignment-immutable    Intercept assignment operations for "immutable"
                        S3 objects.
buildComboProfiles      Build an assay table with an 'S4' object.
buildComboProfiles,LongTable-method
                        Build an assay table with selected assay
                        profiles for drug combinations
buildLongTable          Build a LongTable object
buildLongTable,character-method
                        LongTable build method from character
buildLongTable,data.frame-method
                        LongTable build method
buildLongTable,list-method
                        LongTable build method from list
c.immutable             Intercept concatenation for "immutable" class
                        objects to return another "immutable" class
                        object.
checkColumnCardinality
                        Search a data.frame for 1:'cardinality'
                        relationships between a group of columns (your
                        identifiers) and all other columns.
checkCsetStructure      A function to verify the structure of a CoreSet
clevelandSmall_cSet     Cleaveland_mut RadioSet subsetted and cast as
                        CoreSet
colData,LongTableDataMapper-method
                        Convenience method to subset the 'colData' out
                        of the 'rawdata' slot using the assigned
                        'colDataMap' metadata.
colData,TREDataMapper-method
                        Convenience method to subset the 'colData' out
                        of the 'rawdata' slot using the assigned
                        'colDataMap' metadata.
colIDs                  Generic to access the row identifiers for an
                        object.
collect_fn_params       Collects all function arguments other than the
                        first into a single list parameter.
colMeta                 Generic to access the column identifiers for a
                        rectangular object.
connectivityScore       Function computing connectivity scores between
                        two signatures
CoreGx-deprecated       List of 'deprecated' or 'defunct' methods in
                        the 'CoreGx' R package.
CoreSet                 CoreSet constructor
CoreSet-accessors       Accessing and modifying information in a
                        'CoreSet'
CoreSet-class           CoreSet - A generic data container for
                        molecular profiles and treatment response data
CoreSet-utils           Utility methods for a 'CoreSet' object.
CoreSet2                Make a CoreSet with the updated class structure
cosinePerm              Cosine Permutations
DataMapper-accessors    Accessing and modifying data in a 'DataMapper'
                        object.
DataMapper-class        An S4 Class For Mapping from Raw Experimental
                        Data to a Specific S4 Object
drop_fn_params          Drop parameters from a function and replace
                        them with constants inside the function body.
endoaggregate           Perform aggregation over an S4 object, but
                        return an object of the same class.
endoaggregate,LongTable-method
                        Functional API for endomorphic aggregation over
                        a 'LongTable' or inheriting class
exampleDataMapper       Example LongTableDataMapper
getIntern               Retrieve the specified item from object
                        internal metadata.
guessMapping            Generic for Guessing the Mapping Between Some
                        Raw Data and an S4 Object
guessMapping,LongTableDataMapper-method
                        Guess which columns in raw experiment data map
                        to which dimensions.
gwc                     GWC Score
idCols                  Generic to access the unique id columns in an
                        S4 object used to
immutable               Constructor for "immutable" S3-class property
is_optim_compatible     Check whether a function signature is amenable
                        to optimization via 'stats::optim'.
is.items                Get the types of all items in a list
lapply,MultiAssayExperiment-method
                        lapply lapply method for 'MultiAssayExperiment'
list_OR_LongTable-class
                        A class union to allow multiple types in a
                        CoreSet slot
LongTable               LongTable constructor method
LongTable-accessors     Accessing and modifying information in a
                        'LongTable'
LongTableDataMapper     Constructor for the 'LongTableDataMapper'
                        class, which maps from one or more raw
                        experimental data files to the slots of a
                        'LongTable' object.
LongTableDataMapper-accessors
                        Accessing and modifying data in a
                        'LongTableDataMapper' object.
LongTableDataMapper-class
                        A Class for Mapping Between Raw Data and an
                        'LongTable' Object
make_optim_function     Takes a non-primitive R function and refactors
                        it to be compatible with optimization via
                        'stats::optim'.
mcc                     Compute a Mathews Correlation Coefficient
merckLongTable          Merck Drug Combination Data LongTable
mergeAssays             Merge assays with an 'S4' object.
mergeAssays,LongTable-method
                        Endomorphically merge assays within a
                        'LongTable' or inheriting class
metaConstruct           Generic for preprocessing complex data before
                        being used in the constructor of an 'S4'
                        container object.
metadata,LongTable-method
                        Getter method for the metadata slot of a
                        'LongTable' object
metadata<-,LongTable-method
                        Setter method for the metadata slot of a
                        'LongTable' object
mutable                 Remove the "immutable" S3-class from an R
                        object, allowing it to be modified normally
                        again.
nci_TRE_small           NCI-ALMANAC Drug Combination Data
                        TreatmentResponseExperiment Subset
optimizeCoreGx          A helper method to find the best multithreading
                        configuration for your computer
reindex                 Generic method for resetting indexing in an S4
                        object
reindex,LongTable-method
                        Redo indexing for a LongTable object to remove
                        any gaps in integer indexes
rowData,LongTableDataMapper-method
                        Convenience method to subset the 'rowData' out
                        of the 'rawdata' slot using the assigned
                        'rowDataMap' metadata.
rowData,TREDataMapper-method
                        Convenience method to subset the 'rowData' out
                        of the 'rawdata' slot using the assigned
                        'rowDataMap' metadata.
rowIDs                  Generic to access the row identifiers from
rowMeta                 Generic to access the row identifiers from
sensitivityInfo         Generic function to get the annotations for a
                        treatment response experiment from an S4 class
sensitivityInfo<-       sensitivityInfo<- Generic Method
sensitivityMeasures     sensitivityMeasures Generic
sensitivityMeasures<-   sensitivityMeasures<- Generic
sensitivityProfiles     sensitivityProfiles Generic
sensitivityProfiles<-   sensitivityProfiles<- Generic
sensitivityRaw          sensitivityRaw Generic Method
sensitivityRaw<-        sensitivityRaw<- Generic
sensitivitySlotToLongTable
                        sensitivitySlotToLongTable Generic
setOps-immutable        Subset an immutable object, returning another
                        immutable object.
show,CoreSet-method     Show a CoreSet
show,LongTable-method   Show method for the LongTable class
showSigAnnot            Get the annotations for a 'Signature' class
                        object, as returned by 'drugSensitivitysig' or
                        'radSensitivtySig' functions available in
                        'PharmacoGx' and 'RadioGx', respectively.
subset,LongTable-method
                        Subset method for a LongTable object.
summarizeMolecularProfiles
                        Summarize molecular profile data such that
                        there is a single entry for each sample
                        line/treatment combination
summarizeSensitivityProfiles
                        Summarize across replicates for a sensitivity
                        dose-response experiment
TreatmentResponseExperiment
                        TreatmentResponseExperiment constructor method
TREDataMapper           Constructor for the 'TREDataMapper' class,
                        which maps from one or more raw experimental
                        data files to the slots of a 'LongTable'
                        object.
TREDataMapper-accessors
                        Accessing and modifying data in a
                        'TREDataMapper' object.
TREDataMapper-class     A Class for Mapping Between Raw Data and an
                        'TreatmentResponseExperiment' Object
updateObject,CoreSet-method
                        Update the 'CoreSet' class after changes in it
                        struture or API
updateObject,LongTable-method
                        Update the 'LongTable' class after changes in
                        it struture or API
