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

---

Documentation for package ‘CoreGx’ version 2.6.1

• 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.