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

Documentation for package ‘CoreGx’ version 1.4.2

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-- 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