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

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Documentation for package ‘CoreGx’ version 1.2.0

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A B C D F G I L M N P R S misc

-- A --

amcc Calculate an Adaptive Matthews Correlation Coefficient
annotation-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
annotation<--method annotation<- Slot Setter
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.

-- B --

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

-- C --

cellInfo cellInfo Getter
cellInfo-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
cellInfo<- cellInfo<- Generic
cellInfo<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
cellNames cellNames Generic
cellNames-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
cellNames<- cellNames<- Generic
cellNames<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
checkCsetStructure A function to verify the structure of a CoreSet
clevelandSmall_cSet Cleaveland_mut RadioSet subsetted and cast as CoreSet
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-class A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
cosinePerm Cosine Permutations
curation curation Slot Getter
curation-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
curation<- curation<- Slot Setter
curation<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- D --

datasetType datasetType Generic
datasetType-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
datasetType<- datasetType<- Replacement Generic
datasetType<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
dateCreated dateCreated Generic
dateCreated-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
dateCreated<- dateCreated<- Generic
dateCreated<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- F --

featureInfo featureInfo Generic
featureInfo-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
featureInfo<- featureInfo<- Generic
featureInfo<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
fNames fNames Generic
fNames-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
fNames<- fNames<- Generic
fNames<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- G --

getIntern Retrieve the symbol for the object@.intern slot
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 --

list_or_LongTable-class A class union to allow multiple types in a CoreSet slot
LongTable LongTable constructor method

-- M --

mcc Compute a Mathews Correlation Coefficient
mDataNames mDataNames Generic
mDataNames-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
mDataNames<- mDataNames<- Generic
mDataNames<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
merckLongTable Merck Drug Combination Data LongTable
metadata-method Getter method for the metadata slot of a 'LongTable' object
metadata<--method Setter method for the metadata slot of a 'LongTable' object
molecularProfiles molecularProfiles Generic
molecularProfiles-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
molecularProfiles<- molecularProfiles<- Generic
molecularProfiles<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
molecularProfilesSlot molecularProfilesSlot Generic
molecularProfilesSlot-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
molecularProfilesSlot<- molecularProfilesSlot<-
molecularProfilesSlot<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- N --

name name Generic
name-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
name<- name<- Generic
name<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- P --

pertNumber pertNumber Generic
pertNumber-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
pertNumber<- pertNumber<- Generic
pertNumber<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
phenoInfo phenoInfo Generic
phenoInfo-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
phenoInfo<- phenoInfo<- Generic
phenoInfo<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines

-- R --

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
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 A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityInfo<- sensitivityInfo<- Generic Method
sensitivityInfo<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityMeasures sensitivityMeasures Generic
sensitivityMeasures-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityMeasures<- sensitivityMeasures<- Generic
sensitivityMeasures<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityProfiles sensitivityProfiles Generic
sensitivityProfiles-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityProfiles<- sensitivityProfiles<- Generic
sensitivityProfiles<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityRaw sensitivityRaw Generic Method
sensitivityRaw-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivityRaw<- sensitivityRaw<- Generic
sensitivityRaw<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivitySlot sensitivitySlot Generic
sensitivitySlot-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivitySlot<- sensitivitySlot<- Replacement Generic
sensitivitySlot<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensitivitySlotToLongTable sensitivitySlotToLongTable Generic
sensNumber sensNumber Generic
sensNumber-method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
sensNumber<- sensNumber<- Generic
sensNumber<--method A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
show-method Show a CoreSet
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
. Convenience function for converting R code to a call
.CoreSet A Superclass to Contain Data for Genetic Profiling and Viability Screens of Cancer Cell Lines
[-method [ LongTable Method