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

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Documentation for package ‘CoreGx’ version 2.13.0

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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.