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

## Documentation for package ‘CoreGx’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I L M N P R S 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.LongTable | Coerce a LongTable to a data.frame
as.data.table.LongTable | Coerce a LongTable into a 'data.table'
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.

## -- B --

buildLongTable | Build a LongTable object
buildLongTable-method | LongTable build method from list

## -- C --

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-method | 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
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.
connectivityScore | Function computing connectivity scores between two signatures
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
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'

## -- 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 symbol for the object@.intern slot
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.
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
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'

## -- 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'

## -- 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'

## -- 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.
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
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

## -- S --

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'
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
showSigAnnot | Get the annotations for a 'Signature' class object, as returned by 'drugSensitivitysig' or 'radSensitivtySig' functions available in 'PharmacoGx' and 'RadioGx', respectively.
subset-method | Subset method for a LongTable object.
summarizeMolecularProfiles | Summarize molecular profile data such that there is a single entry for each cell line/treatment combination
summarizeSensitivityProfiles | Summarize across replicates for a sensitivity dose-response experiment

## -- misc --

$-method | Select an assay from a LongTable object
$<--method | Update an assay from a LongTable object
. | Convenience function for converting R code to a call
.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
[-method | [ LongTable Method
[[<--method | [[<- Method for LongTable Class