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

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

## Documentation for package ‘CoreGx’ version 2.17.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G I L M N O P R S T U misc

## -- A --

aggregate-method | Functional API for aggregation over a 'LongTable' or inheriting class
aggregate-method | Functional S4 API for aggregation over a 'data.table' object.
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
annotation | Accessing and modifying information in a 'CoreSet'
annotation-method | Accessing and modifying information in a 'CoreSet'
annotation<- | Accessing and modifying information in a 'CoreSet'
annotation<--method | Accessing and modifying information in a 'CoreSet'
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
assayMap | Accessing and modifying data in a 'TREDataMapper' object.
assayMap-method | Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap-method | Accessing and modifying data in a 'TREDataMapper' object.
assayMap<- | Accessing and modifying data in a 'TREDataMapper' object.
assayMap<-,LongTableDataMapper,List-methhod | Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap<-,TREDataMapper,List-methhod | Accessing and modifying data in a 'TREDataMapper' object.
assayMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap<--method | Accessing and modifying data in a 'TREDataMapper' object.
assignment-immutable | Intercept assignment operations for "immutable" S3 objects.

## -- B --

buildComboProfiles | Build an assay table with an 'S4' object.
buildComboProfiles-method | Build an assay table with selected assay profiles for drug combinations
buildLongTable | Build a LongTable object
buildLongTable-method | LongTable build method from character
buildLongTable-method | LongTable build method
buildLongTable-method | LongTable build method from list

## -- C --

c.immutable | Intercept concatenation for "immutable" class objects to return another "immutable" class object.
cardinality | Search a data.frame for 1:'cardinality' relationships between a group of columns (your identifiers) and all other columns.
cellInfo | Accessing and modifying information in a 'CoreSet'
cellInfo-method | Accessing and modifying information in a 'CoreSet'
cellInfo<- | Accessing and modifying information in a 'CoreSet'
cellInfo<--method | Accessing and modifying information in a 'CoreSet'
cellName-method | Accessing and modifying information in a 'CoreSet'
cellNames | Accessing and modifying information in a 'CoreSet'
cellNames<- | Accessing and modifying information in a 'CoreSet'
cellNames<--method | Accessing and modifying information in a 'CoreSet'
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-method | Convenience method to subset the 'colData' out of the 'rawdata' slot using the assigned 'colDataMap' metadata.
colData-method | Convenience method to subset the 'colData' out of the 'rawdata' slot using the assigned 'colDataMap' metadata.
colDataMap | Accessing and modifying data in a 'TREDataMapper' object.
colDataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap-method | Accessing and modifying data in a 'TREDataMapper' object.
colDataMap<- | Accessing and modifying data in a 'TREDataMapper' object.
colDataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap<--method | Accessing and modifying data in a 'TREDataMapper' object.
colDataMap<-LongTableDataMapper-method | Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap<-TREDataMapper-method | Accessing and modifying data in a 'TREDataMapper' object.
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.
colnames<- | Intercept assignment operations for "immutable" S3 objects.
colnames<-.immutable | Intercept assignment operations for "immutable" S3 objects.
colnames<-.immutable, | Intercept assignment operations for "immutable" S3 objects.
connectivityScore | Function computing connectivity scores between two signatures
CoreGx-defunct | List of 'deprecated' or 'defunct' methods in the 'CoreGx' R package.
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
curation | Accessing and modifying information in a 'CoreSet'
curation-method | Accessing and modifying information in a 'CoreSet'
curation<- | Accessing and modifying information in a 'CoreSet'
curation<--method | Accessing and modifying information in a 'CoreSet'

## -- D --

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
datasetType | Accessing and modifying information in a 'CoreSet'
datasetType-method | Accessing and modifying information in a 'CoreSet'
datasetType<- | Accessing and modifying information in a 'CoreSet'
datasetType<--method | Accessing and modifying information in a 'CoreSet'
dateCreated | Accessing and modifying information in a 'CoreSet'
dateCreated-method | Accessing and modifying information in a 'CoreSet'
dateCreated<- | Accessing and modifying information in a 'CoreSet'
dateCreated<--method | Accessing and modifying information in a 'CoreSet'
dimnames<- | Intercept assignment operations for "immutable" S3 objects.
dimnames<-.immutable | Intercept assignment operations for "immutable" S3 objects.
dimnames<-.immutable, | Intercept assignment operations for "immutable" S3 objects.
drop_fn_params | Drop parameters from a function and replace them with constants inside the function body.

## -- E --

endoaggregate | Perform aggregation over an S4 object, but return an object of the same class.
endoaggregate-method | Functional API for endomorphic aggregation over a 'LongTable' or inheriting class
exampleDataMapper | Example LongTableDataMapper

## -- F --

featureInfo | Accessing and modifying information in a 'CoreSet'
featureInfo-method | Accessing and modifying information in a 'CoreSet'
featureInfo<- | Accessing and modifying information in a 'CoreSet'
featureInfo<--method | Accessing and modifying information in a 'CoreSet'
fNames | Accessing and modifying information in a 'CoreSet'
fNames-method | Accessing and modifying information in a 'CoreSet'
fNames<- | Accessing and modifying information in a 'CoreSet'
fNames<--method | Accessing and modifying information in a 'CoreSet'

## -- G --

getIntern | Retrieve the specified item from object internal metadata.
guessMapping | Generic for Guessing the Mapping Between Some Raw Data and an S4 Object
guessMapping-method | Guess which columns in raw experiment data map to which dimensions.
gwc | GWC Score

## -- I --

idCols | Generic to access the unique id columns in an S4 object used to
immutable | Constructor for "immutable" S3-class property
immutable_list-class | Constructor for "immutable" S3-class property
is.immutable | Constructor for "immutable" S3-class property
is.items | Get the types of all items in a list
is_optim_compatible | Check whether a function signature is amenable to optimization via 'stats::optim'.

## -- L --

lapply-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

## -- M --

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
mDataNames | Accessing and modifying information in a 'CoreSet'
mDataNames-method | Accessing and modifying information in a 'CoreSet'
mDataNames<- | Accessing and modifying information in a 'CoreSet'
mDataNames<--method | Accessing and modifying information in a 'CoreSet'
merckLongTable | Merck Drug Combination Data LongTable
mergeAssays | Merge assays with an 'S4' object.
mergeAssays-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.
metaConstruct-method | Generic for preprocessing complex data before being used in the constructor of an 'S4' container object.
metadata-method | Getter method for the metadata slot of a 'LongTable' object
metadata<--method | Setter method for the metadata slot of a 'LongTable' object
metadataMap | Accessing and modifying data in a 'TREDataMapper' object.
metadataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object.
metadataMap-method | Accessing and modifying data in a 'TREDataMapper' object.
metadataMap<- | Accessing and modifying data in a 'TREDataMapper' object.
metadataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object.
metadataMap<--method | Accessing and modifying data in a 'TREDataMapper' object.
molecularProfiles | Accessing and modifying information in a 'CoreSet'
molecularProfiles-method | Accessing and modifying information in a 'CoreSet'
molecularProfiles<- | Accessing and modifying information in a 'CoreSet'
molecularProfiles<--method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot-method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<- | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<--method | Accessing and modifying information in a 'CoreSet'
molecularProfilesSlot<-CoreSet-method | Accessing and modifying information in a 'CoreSet'
moleculerProfilesSlot-method | Accessing and modifying information in a 'CoreSet'
mutable | Remove the "immutable" S3-class from an R object, allowing it to be modified normally again.

## -- N --

name | Accessing and modifying information in a 'CoreSet'
name-method | Accessing and modifying information in a 'CoreSet'
name<- | Accessing and modifying information in a 'CoreSet'
name<--method | Accessing and modifying information in a 'CoreSet'
names<- | Intercept assignment operations for "immutable" S3 objects.
names<-.immutable | Intercept assignment operations for "immutable" S3 objects.
nci_TRE_small | NCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset

## -- O --

optimizeCoreGx | A helper method to find the best multithreading configuration for your computer

## -- P --

pertNumber | Accessing and modifying information in a 'CoreSet'
pertNumber-method | Accessing and modifying information in a 'CoreSet'
pertNumber<- | Accessing and modifying information in a 'CoreSet'
pertNumber<--method | Accessing and modifying information in a 'CoreSet'
phenoInfo | Accessing and modifying information in a 'CoreSet'
phenoInfo-method | Accessing and modifying information in a 'CoreSet'
phenoInfo<- | Accessing and modifying information in a 'CoreSet'
phenoInfo<--method | Accessing and modifying information in a 'CoreSet'
print.immutable | Constructor for "immutable" S3-class property

## -- R --

rawdata | Accessing and modifying data in a 'DataMapper' object.
rawdata-method | Accessing and modifying data in a 'DataMapper' object.
rawdata-method | Accessing and modifying data in a 'LongTableDataMapper' object.
rawdata-method | Accessing and modifying data in a 'TREDataMapper' object.
rawdata<- | Accessing and modifying data in a 'DataMapper' object.
rawdata<--method | Accessing and modifying data in a 'DataMapper' object.
rawdata<--method | Accessing and modifying data in a 'LongTableDataMapper' object.
rawdata<--method | Accessing and modifying data in a 'TREDataMapper' object.
reindex | Generic method for resetting indexing in an S4 object
reindex-method | Redo indexing for a LongTable object to remove any gaps in integer indexes
rowData-method | Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata.
rowData-method | Convenience method to subset the 'rowData' out of the 'rawdata' slot using the assigned 'rowDataMap' metadata.
rowDataMap | Accessing and modifying data in a 'TREDataMapper' object.
rowDataMap-method | Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap-method | Accessing and modifying data in a 'TREDataMapper' object.
rowDataMap<- | Accessing and modifying data in a 'TREDataMapper' object.
rowDataMap<--method | Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap<--method | Accessing and modifying data in a 'TREDataMapper' object.
rowDataMap<-LongTableDataMapper-method | Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap<-TREDataMapper-method | Accessing and modifying data in a 'TREDataMapper' object.
rowIDs | Generic to access the row identifiers from
rowMeta | Generic to access the row identifiers from
rownames<- | Intercept assignment operations for "immutable" S3 objects.
rownames<-.immutable | Intercept assignment operations for "immutable" S3 objects.
rownames<-.immutable, | Intercept assignment operations for "immutable" S3 objects.

## -- S --

sampleInfo | Accessing and modifying information in a 'CoreSet'
sampleInfo-method | Accessing and modifying information in a 'CoreSet'
sampleInfo<- | Accessing and modifying information in a 'CoreSet'
sampleInfo<--method | Accessing and modifying information in a 'CoreSet'
sampleName-method | Accessing and modifying information in a 'CoreSet'
sampleNames | Accessing and modifying information in a 'CoreSet'
sampleNames-method | Accessing and modifying information in a 'CoreSet'
sampleNames<- | Accessing and modifying information in a 'CoreSet'
sampleNames<--method | Accessing and modifying information in a 'CoreSet'
sensitivityInfo | Generic function to get the annotations for a treatment response experiment from an S4 class
sensitivityInfo-method | Accessing and modifying information in a 'CoreSet'
sensitivityInfo<- | sensitivityInfo<- Generic Method
sensitivityInfo<--method | Accessing and modifying information in a 'CoreSet'
sensitivityMeasures | sensitivityMeasures Generic
sensitivityMeasures-method | Accessing and modifying information in a 'CoreSet'
sensitivityMeasures<- | sensitivityMeasures<- Generic
sensitivityMeasures<--method | Accessing and modifying information in a 'CoreSet'
sensitivityProfiles | sensitivityProfiles Generic
sensitivityProfiles-method | Accessing and modifying information in a 'CoreSet'
sensitivityProfiles<- | sensitivityProfiles<- Generic
sensitivityProfiles<--method | Accessing and modifying information in a 'CoreSet'
sensitivityRaw | sensitivityRaw Generic Method
sensitivityRaw-method | Accessing and modifying information in a 'CoreSet'
sensitivityRaw<- | sensitivityRaw<- Generic
sensitivityRaw<--method | Accessing and modifying information in a 'CoreSet'
sensitivitySlot | Accessing and modifying information in a 'CoreSet'
sensitivitySlot<- | Accessing and modifying information in a 'CoreSet'
sensitivitySlotToLongTable | sensitivitySlotToLongTable Generic
sensitvityInfo<--method | Accessing and modifying information in a 'CoreSet'
sensNumber | Accessing and modifying information in a 'CoreSet'
sensNumber-method | Accessing and modifying information in a 'CoreSet'
sensNumber<- | Accessing and modifying information in a 'CoreSet'
sensNumber<--method | Accessing and modifying information in a 'CoreSet'
setOps-immutable | Subset an immutable object, returning another immutable object.
show-method | A Class for Mapping Between Raw Data and an 'LongTable' Object
show-method | Show a CoreSet
show-method | Show method for the LongTable class
show.immutable | Constructor for "immutable" S3-class property
showSigAnnot | Get the annotations for a 'Signature' class object, as returned by 'drugSensitivitysig' or 'radSensitivtySig' functions available in 'PharmacoGx' and 'RadioGx', respectively.
subset, | Subset an immutable object, returning another immutable object.
subset-method | Subset method for a LongTable object.
subset.immutable | Subset an immutable object, returning another immutable object.
subset<-.immutable | Intercept assignment operations for "immutable" S3 objects.
subset<-.immutable, | Intercept assignment operations for "immutable" S3 objects.
subsetByFeature | Utility methods for a 'CoreSet' object.
subsetByFeature-method | Utility methods for a 'CoreSet' object.
subsetBySample | Utility methods for a 'CoreSet' object.
subsetBySample-method | Utility methods for a 'CoreSet' object.
subsetByTreatment | Utility methods for a 'CoreSet' object.
subsetByTreatment-method | Utility methods for a 'CoreSet' 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

## -- T --

treamentResponse<--method | Accessing and modifying information in a 'CoreSet'
treatmentInfo | Accessing and modifying information in a 'CoreSet'
treatmentInfo-method | Accessing and modifying information in a 'CoreSet'
treatmentInfo<- | Accessing and modifying information in a 'CoreSet'
treatmentInfo<--method | Accessing and modifying information in a 'CoreSet'
treatmentNames | Accessing and modifying information in a 'CoreSet'
treatmentNames-method | Accessing and modifying information in a 'CoreSet'
treatmentNames<- | Accessing and modifying information in a 'CoreSet'
treatmentNames<--method | Accessing and modifying information in a 'CoreSet'
treatmentResponse | Accessing and modifying information in a 'CoreSet'
treatmentResponse-method | Accessing and modifying information in a 'CoreSet'
treatmentResponse<- | Accessing and modifying information in a 'CoreSet'
treatmentResponse<--method | Accessing and modifying information in a 'CoreSet'
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

## -- U --

updateObject-method | Update the 'CoreSet' class after changes in it struture or API
updateObject-method | Update the 'LongTable' class after changes in it struture or API

## -- misc --

$ | Subset an immutable object, returning another immutable object.
$-method | Select an assay from a LongTable object
$.immutable | Subset an immutable object, returning another immutable object.
$<- | Intercept assignment operations for "immutable" S3 objects.
$<--method | Update an assay from a LongTable object
$<-.immubtale, | Intercept assignment operations for "immutable" S3 objects.
$<-.immutable | Intercept assignment operations for "immutable" S3 objects.
. | Convenience function for converting R code to a call
.assayToBumpyMatrix | Convert a LongTable assay into a BumpyMatrix object
.CoreSet | CoreSet - A generic data container for molecular profiles and treatment response data
.DataMapper | An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object
.fitCurve2 | Curve fitting via 'stats::optim' L-BFGS-B with fall-back grid/pattern search if convergence is not achieved.
.LongTableDataMapper | A Class for Mapping Between Raw Data and an 'LongTable' Object
.longTableToSummarizedExperiment | Convert LongTable to gDR Style SummarizedExperiment
.TREDataMapper | A Class for Mapping Between Raw Data and an 'TreatmentResponseExperiment' Object
[ | Subset an immutable object, returning another immutable object.
[-method | [ LongTable Method
[.immutable | Subset an immutable object, returning another immutable object.
[.immutable, | Subset an immutable object, returning another immutable object.
[<- | Intercept assignment operations for "immutable" S3 objects.
[<-.immutable | Intercept assignment operations for "immutable" S3 objects.
[<-.immutable, | Intercept assignment operations for "immutable" S3 objects.
[[ | Subset an immutable object, returning another immutable object.
[[.immutable | Subset an immutable object, returning another immutable object.
[[.immutable, | Subset an immutable object, returning another immutable object.
[[<- | Intercept assignment operations for "immutable" S3 objects.
[[<--method | [[<- Method for LongTable Class
[[<-.immutable | Intercept assignment operations for "immutable" S3 objects.
[[<-.immutable, | Intercept assignment operations for "immutable" S3 objects.