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CoreGx-deprecated CoreGx-defunct
List of deprecated or defunct methods in the CoreGx R package.
annotation(<CoreSet> ) `annotation<-`(<CoreSet> ,<list> ) dateCreated(<CoreSet> ) `dateCreated<-`(<CoreSet> ,<character> ) name(<CoreSet> ) `name<-`(<CoreSet> ) sampleInfo(<CoreSet> ) `sampleInfo<-`(<CoreSet> ,<data.frame> ) sampleNames(<CoreSet> ) `sampleNames<-`(<CoreSet> ,<character> ) treatmentInfo(<CoreSet> ) `treatmentInfo<-`(<CoreSet> ,<data.frame> ) treatmentNames(<CoreSet> ) `treatmentNames<-`(<CoreSet> ,<character> ) curation(<CoreSet> ) `curation<-`(<CoreSet> ,<list> ) datasetType(<CoreSet> ) `datasetType<-`(<CoreSet> ,<character> ) molecularProfiles(<CoreSet> ) `molecularProfiles<-`(<CoreSet> ,<character> ,<character> ,<matrix> ) `molecularProfiles<-`(<CoreSet> ,<character> ,<missing> ,<matrix> ) `molecularProfiles<-`(<CoreSet> ,<missing> ,<missing> ,<list_OR_MAE> ) featureInfo(<CoreSet> ) `featureInfo<-`(<CoreSet> ,<character> ,<data.frame> ) phenoInfo(<CoreSet> ,<character> ) `phenoInfo<-`(<CoreSet> ,<character> ,<data.frame> ) fNames(<CoreSet> ,<character> ) `fNames<-`(<CoreSet> ,<character> ,<character> ) mDataNames(<CoreSet> ) `mDataNames<-`(<CoreSet> ) molecularProfilesSlot(<CoreSet> ) `molecularProfilesSlot<-`(<CoreSet> ,<list_OR_MAE> ) sensitivityInfo(<CoreSet> ) `sensitivityInfo<-`(<CoreSet> ,<data.frame> ) sensitivityMeasures(<CoreSet> ) `sensitivityMeasures<-`(<CoreSet> ,<character> ) sensitivityProfiles(<CoreSet> ) `sensitivityProfiles<-`(<CoreSet> ,<data.frame> ) sensitivityRaw(<CoreSet> ) `sensitivityRaw<-`(<CoreSet> ,<array> ) treatmentResponse(<CoreSet> ) `treatmentResponse<-`(<CoreSet> ,<list_OR_LongTable> ) sensNumber(<CoreSet> ) `sensNumber<-`(<CoreSet> ,<matrix> ) pertNumber(<CoreSet> ) `pertNumber<-`(<CoreSet> ,<array> )
Accessing and modifying information in a CoreSet
CoreSet-class .CoreSet
CoreSet - A generic data container for molecular profiles and
treatment response data
subsetBySample(<CoreSet> ) subsetByTreatment(<CoreSet> ) subsetByFeature(<CoreSet> )
Utility methods for a CoreSet object.
CoreSet()
CoreSet constructor
CoreSet2()
Make a CoreSet with the updated class structure
rawdata(<DataMapper> ) `rawdata<-`(<DataMapper> ,<ANY> )
Accessing and modifying data in a DataMapper object.
DataMapper-class .DataMapper
An S4 Class For Mapping from Raw Experimental Data to a Specific S4 Object
LongTable-accessors
Accessing and modifying information in a LongTable
LongTable()
LongTable constructor method
`rawdata<-`(<LongTableDataMapper> ,<list> ) rowDataMap(<LongTableDataMapper> ) `rowDataMap<-`(<LongTableDataMapper> ,<list_OR_List> ) colDataMap(<LongTableDataMapper> ) `colDataMap<-`(<LongTableDataMapper> ,<list_OR_List> ) assayMap(<LongTableDataMapper> ) `assayMap<-`(<LongTableDataMapper> ,<list_OR_List> ) metadataMap(<LongTableDataMapper> ) `metadataMap<-`(<LongTableDataMapper> ,<list_OR_List> )
Accessing and modifying data in a LongTableDataMapper object.
show(<LongTableDataMapper> )
A Class for Mapping Between Raw Data and an LongTable Object
LongTableDataMapper()
Constructor for the LongTableDataMapper class, which maps from one or
more raw experimental data files to the slots of a LongTable object.
`rawdata<-`(<TREDataMapper> ,<list> ) rowDataMap(<TREDataMapper> ) `rowDataMap<-`(<TREDataMapper> ,<list_OR_List> ) colDataMap(<TREDataMapper> ) `colDataMap<-`(<TREDataMapper> ,<list_OR_List> ) assayMap(<TREDataMapper> ) `assayMap<-`(<TREDataMapper> ,<list_OR_List> ) metadataMap(<TREDataMapper> ) `metadataMap<-`(<TREDataMapper> ,<list_OR_List> )
Accessing and modifying data in a TREDataMapper object.
TREDataMapper-class .TREDataMapper
A Class for Mapping Between Raw Data and an TreatmentResponseExperiment
Object
TREDataMapper()
Constructor for the TREDataMapper class, which maps from one or
more raw experimental data files to the slots of a LongTable object.
TreatmentResponseExperiment()
TreatmentResponseExperiment constructor method
aggregate(<LongTable> )
Functional API for aggregation over a LongTable or inheriting class
aggregate(<data.table> )
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
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 subset subset [ [[ $ colnames rownames dimnames names [ [ [[ [[ $ $ names dimnames dimnames colnames colnames rownames rownames
Intercept assignment operations for "immutable" S3 objects.
buildComboProfiles(<LongTable> )
Build an assay table with selected assay profiles for drug combinations
buildComboProfiles()
Build an assay table with an S4 object.
buildLongTable(<character> )
LongTable build method from character
buildLongTable(<data.frame> )
LongTable build method
buildLongTable(<list> )
LongTable build method from list
buildLongTable()
Build a LongTable object
c(<immutable> )
Intercept concatenation for "immutable" class objects to return another "immutable" class object.
`$`(<LongTable> )
Select an assay from a LongTable object
`$<-`(<LongTable> )
Update an assay from a LongTable 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> )
Convenience method to subset the colData out of the rawdata slot using
the assigned colDataMap metadata.
colData(<TREDataMapper> )
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.
colMeta()
Generic to access the column identifiers for a rectangular object.
collect_fn_params()
Collects all function arguments other than the first into a single list
parameter.
connectivityScore()
Function computing connectivity scores between two signatures
cosinePerm()
Cosine Permutations
.()
Convenience function for converting R code to a call
.assayToBumpyMatrix()
Convert a LongTable assay into a BumpyMatrix object
.fitCurve2()
Curve fitting via stats::optim
.longTableToSummarizedExperiment()
Convert LongTable to gDR Style SummarizedExperiment
drop_fn_params()
Drop parameters from a function and replace them with constants
inside the function body.
endoaggregate(<LongTable> )
Functional API for endomorphic aggregation over a LongTable or
inheriting class
endoaggregate()
Perform aggregation over an S4 object, but return an object of the same
class.
exampleDataMapper
Example LongTableDataMapper
getIntern()
Retrieve the specified item from object internal metadata.
guessMapping(<LongTableDataMapper> )
Guess which columns in raw experiment data map to which dimensions.
guessMapping()
Generic for Guessing the Mapping Between Some Raw Data and an S4 Object
gwc()
GWC Score
idCols()
Generic to access the unique id columns in an S4 object used to
immutable() is.immutable() print(<immutable> ) show.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
lapply(<MultiAssayExperiment> )
lapply
lapply method for MultiAssayExperiment
list_OR_LongTable-class
Function to combine two LongTables into a single LongTable
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(<LongTable> )
Endomorphically merge assays within a LongTable or inheriting class
mergeAssays()
Merge assays with an S4 object.
metaConstruct()
Generic for preprocessing complex data before being used in the constructor
of an S4 container object.
metadata(<LongTable> )
Getter method for the metadata slot of a LongTable object
`metadata<-`(<LongTable> )
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(<LongTable> )
Redo indexing for a LongTable object to remove any gaps in integer indexes
reindex()
Generic method for resetting indexing in an S4 object
rowData(<LongTableDataMapper> )
Convenience method to subset the rowData out of the rawdata slot using
the assigned rowDataMap metadata.
rowData(<TREDataMapper> )
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<-`()
sensitivityInfo<- Generic Method
sensitivityInfo()
Generic function to get the annotations for a treatment response experiment
from an S4 class
`sensitivityMeasures<-`()
sensitivityMeasures<- Generic
sensitivityMeasures()
sensitivityMeasures Generic
`sensitivityProfiles<-`()
sensitivityProfiles<- Generic
sensitivityProfiles()
sensitivityProfiles Generic
`sensitivityRaw<-`()
sensitivityRaw<- Generic
sensitivityRaw()
sensitivityRaw Generic Method
sensitivitySlotToLongTable()
sensitivitySlotToLongTable Generic
subset.immutable() `[`(<immutable> ) `[[`(<immutable> ) `$`(<immutable> )
Subset an immutable object, returning another immutable object.
show(<CoreSet> )
Show a CoreSet
show(<LongTable> )
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.
`[`(<LongTable> ,<ANY> ,<ANY> ,<ANY> )
[ LongTable Method
`[[<-`(<LongTable> ,<ANY> ,<ANY> )
[[<- Method for LongTable Class
subset(<LongTable> )
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
updateObject(<CoreSet> )
Update the CoreSet class after changes in it struture or API
updateObject(<LongTable> )
Update the LongTable class after changes in it struture or API