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


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Documentation for package ‘CoreGx’ version 2.0.2

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

-- A --

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 LongTable to data.table conversion
as.data.frame.long.table LongTable to data.table conversion
as.data.table.long.table LongTable to data.table conversion
as.long.table Coerce from data.table to LongTable
assayCols Generic to access the assay columns of a rectangular object.
assayMap Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap-method Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap<- Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap<-,LongTableDataMapper,List-methhod Accessing and modifying data in a 'LongTableDataMapper' object.
assayMap<--method Accessing and modifying data in a 'LongTableDataMapper' object.
assignment-immutable Intercept assignment operations for "immutable" S3 objects.

-- B --

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.
colDataMap Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap-method Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap<- Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap<--method Accessing and modifying data in a 'LongTableDataMapper' object.
colDataMap<-LongTableDataMapper-method Accessing and modifying data in a 'LongTableDataMapper' object.
colIDs Generic to access the row identifiers for an object.
colMeta Generic to access the column identifiers for a rectangular object.
colnames<- Intercept assignment operations for "immutable" S3 objects.
colnames<-, 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<-, Intercept assignment operations for "immutable" S3 objects.
dimnames<-.immutable Intercept assignment operations for "immutable" S3 objects.

-- E --

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
idCols-method Retrieve the unique identifier columns used for primary keys in rowData and colData.
immutable Constructor for "immutable" S3-class property
immutable_list-class Constructor for "immutable" S3-class property
is.immutable Check if an R object inherits from the immutable S3-class.
is.items Get the types of all items in a list

-- 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 --

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
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 'LongTableDataMapper' object.
metadataMap-method Accessing and modifying data in a 'LongTableDataMapper' object.
metadataMap<- Accessing and modifying data in a 'LongTableDataMapper' object.
metadataMap<--method Accessing and modifying data in a 'LongTableDataMapper' 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.

-- 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 Print method for objects inheriting from the "immutable" S3-class

-- 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<- 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.
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.
rowDataMap Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap-method Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap<- Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap<--method Accessing and modifying data in a 'LongTableDataMapper' object.
rowDataMap<-LongTableDataMapper-method Accessing and modifying data in a 'LongTableDataMapper' 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<-, 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-method Accessing and modifying information in a 'CoreSet'
sensitivitySlot<- Accessing and modifying information in a 'CoreSet'
sensitivitySlot<--method 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<-, 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 --

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'
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-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.
$<-, Intercept assignment operations for "immutable" S3 objects.
$<--method Update an assay from a LongTable object
$<-.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
.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.
[, Subset an immutable object, returning another immutable object.
[-method [ LongTable Method
[.immutable Subset an immutable object, returning another immutable object.
[<- Intercept assignment operations for "immutable" S3 objects.
[<-, Intercept assignment operations for "immutable" S3 objects.
[<-.immutable Intercept assignment operations for "immutable" S3 objects.
[[ Subset an immutable object, returning another immutable object.
[[, Subset an immutable object, returning another immutable object.
[[.immutable Subset an immutable object, returning another immutable object.
[[<- Intercept assignment operations for "immutable" S3 objects.
[[<-, Intercept assignment operations for "immutable" S3 objects.
[[<--method [[<- Method for LongTable Class
[[<-.immutable Intercept assignment operations for "immutable" S3 objects.