Analysis of Large-Scale Radio-Genomic Data

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Documentation for package ‘RadioGx’ version 2.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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A C D F L M N P R S T U misc

-- A --

annotation	Accessing and modifying information in a 'RadioSet'
annotation-method	Accessing and modifying information in a 'RadioSet'
annotation<-	Accessing and modifying information in a 'RadioSet'
annotation<--method	Accessing and modifying information in a 'RadioSet'
availableRSets	Return a table of RadioSets available for download

-- C --

cellInfo	Accessing and modifying information in a 'RadioSet'
cellInfo-method	Accessing and modifying information in a 'RadioSet'
cellInfo<-	Accessing and modifying information in a 'RadioSet'
cellInfo<--method	Accessing and modifying information in a 'RadioSet'
cellName-method	Accessing and modifying information in a 'RadioSet'
cellNames	Accessing and modifying information in a 'RadioSet'
cellNames<-	Accessing and modifying information in a 'RadioSet'
cellNames<--method	Accessing and modifying information in a 'RadioSet'
checkRSetStructure	A function to verify the structure of a RadioSet
clevelandSmall	Cleaveland_mut RadioSet subsetted
computeAUC	computeAUC: computes AUC
computeD10	Compute D10
computeSF2	Compute SF2
curation	Accessing and modifying information in a 'RadioSet'
curation-method	Accessing and modifying information in a 'RadioSet'
curation<-	Accessing and modifying information in a 'RadioSet'
curation<--method	Accessing and modifying information in a 'RadioSet'

-- D --

datasetType	Accessing and modifying information in a 'RadioSet'
datasetType-method	Accessing and modifying information in a 'RadioSet'
datasetType<-	Accessing and modifying information in a 'RadioSet'
datasetType<--method	Accessing and modifying information in a 'RadioSet'
dateCreated	Accessing and modifying information in a 'RadioSet'
dateCreated-method	Accessing and modifying information in a 'RadioSet'
dateCreated<-	Accessing and modifying information in a 'RadioSet'
dateCreated<--method	Accessing and modifying information in a 'RadioSet'
dim-method	Get the dimensions of a RadioSet
doseResponseCurve	Plot drug response curve of a given drug and a given cell for a list of rSets (objects of the RadioSet class).
downloadRSet	Download a RadioSet object

-- F --

featureInfo	Accessing and modifying information in a 'RadioSet'
featureInfo-method	Accessing and modifying information in a 'RadioSet'
featureInfo<-	Accessing and modifying information in a 'RadioSet'
featureInfo<--method	Accessing and modifying information in a 'RadioSet'
fNames	Accessing and modifying information in a 'RadioSet'
fNames-method	Accessing and modifying information in a 'RadioSet'
fNames<-	Accessing and modifying information in a 'RadioSet'
fNames<--method	Accessing and modifying information in a 'RadioSet'

-- L --

linearQuadraticModel

Fit linear-quadratic curves to dose-response data

-- M --

mDataNames	Accessing and modifying information in a 'RadioSet'
mDataNames-method	Accessing and modifying information in a 'RadioSet'
mDataNames<-	Accessing and modifying information in a 'RadioSet'
mDataNames<--method	Accessing and modifying information in a 'RadioSet'
molecularProfiles	Accessing and modifying information in a 'RadioSet'
molecularProfiles-method	Accessing and modifying information in a 'RadioSet'
molecularProfiles<-	Accessing and modifying information in a 'RadioSet'
molecularProfiles<--method	Accessing and modifying information in a 'RadioSet'
molecularProfilesSlot	Accessing and modifying information in a 'RadioSet'
molecularProfilesSlot-method	Accessing and modifying information in a 'RadioSet'
molecularProfilesSlot<-	Accessing and modifying information in a 'RadioSet'
molecularProfilesSlot<--method	Accessing and modifying information in a 'RadioSet'
molecularProfilesSlot<-RadioSet-method	Accessing and modifying information in a 'RadioSet'
moleculerProfilesSlot-method	Accessing and modifying information in a 'RadioSet'

-- N --

name	Accessing and modifying information in a 'RadioSet'
name-method	Accessing and modifying information in a 'RadioSet'
name<-	Accessing and modifying information in a 'RadioSet'
name<--method	Accessing and modifying information in a 'RadioSet'

-- P --

pertNumber	Accessing and modifying information in a 'RadioSet'
pertNumber-method	Accessing and modifying information in a 'RadioSet'
pertNumber<-	Accessing and modifying information in a 'RadioSet'
pertNumber<--method	Accessing and modifying information in a 'RadioSet'
phenoInfo	Accessing and modifying information in a 'RadioSet'
phenoInfo-method	Accessing and modifying information in a 'RadioSet'
phenoInfo<-	Accessing and modifying information in a 'RadioSet'
phenoInfo<--method	Accessing and modifying information in a 'RadioSet'
plotCurve	Plot radiation dose-response curve

-- R --

radiationInfo	Accessing and modifying information in a 'RadioSet'
radiationInfo<-	Accessing and modifying information in a 'RadioSet'
radiationTypes	Accessing and modifying information in a 'RadioSet'
radiationTypes<-	Accessing and modifying information in a 'RadioSet'
RadioSet	RadioSet constructor
RadioSet-accessors	Accessing and modifying information in a 'RadioSet'
RadioSet-class	A Class to Contain RadioGenomic datasets together with their curations
RadioSig	Radiation Signature Class Constructor
radSensitivitySig	Creates a signature representing the association between gene expression (or other molecular profile) and radiation dose response, for use in radiation sensitivity analysis.

-- S --

sampleInfo	Accessing and modifying information in a 'RadioSet'
sampleInfo-method	Accessing and modifying information in a 'RadioSet'
sampleInfo<-	Accessing and modifying information in a 'RadioSet'
sampleInfo<--method	Accessing and modifying information in a 'RadioSet'
sampleName-method	Accessing and modifying information in a 'RadioSet'
sampleNames	Accessing and modifying information in a 'RadioSet'
sampleNames-method	Accessing and modifying information in a 'RadioSet'
sampleNames<-	Accessing and modifying information in a 'RadioSet'
sampleNames<--method	Accessing and modifying information in a 'RadioSet'
sensitivityInfo-method	Accessing and modifying information in a 'RadioSet'
sensitivityInfo<--method	Accessing and modifying information in a 'RadioSet'
sensitivityMeasures-method	Accessing and modifying information in a 'RadioSet'
sensitivityMeasures<--method	Accessing and modifying information in a 'RadioSet'
sensitivityProfiles-method	Accessing and modifying information in a 'RadioSet'
sensitivityProfiles<--method	Accessing and modifying information in a 'RadioSet'
sensitivityRaw-method	Accessing and modifying information in a 'RadioSet'
sensitivityRaw<--method	Accessing and modifying information in a 'RadioSet'
sensitivitySlot	Accessing and modifying information in a 'RadioSet'
sensitivitySlot<-	Accessing and modifying information in a 'RadioSet'
sensitvityInfo<--method	Accessing and modifying information in a 'RadioSet'
sensNumber	Accessing and modifying information in a 'RadioSet'
sensNumber-method	Accessing and modifying information in a 'RadioSet'
sensNumber<-	Accessing and modifying information in a 'RadioSet'
sensNumber<--method	Accessing and modifying information in a 'RadioSet'
show-method	Show a RadioSet
show-method	Show RadioGx Signatures
showSigAnnot-method	Show the Annotations of a signature object
subsetTo-method	A function to subset a RadioSet to data containing only specified radiations, cells and genes
summarizeMolecularProfiles-method	Takes molecular data from a RadioSet, and summarises them into one entry per drug
summarizeSensitivityProfiles-method	Takes the sensitivity data from a RadioSet, and summarises them into a drug vs cell line table

-- T --

treamentResponse<--method	Accessing and modifying information in a 'RadioSet'
treatmentInfo	Accessing and modifying information in a 'RadioSet'
treatmentInfo-method	Accessing and modifying information in a 'RadioSet'
treatmentInfo<-	Accessing and modifying information in a 'RadioSet'
treatmentInfo<--method	Accessing and modifying information in a 'RadioSet'
treatmentNames	Accessing and modifying information in a 'RadioSet'
treatmentNames-method	Accessing and modifying information in a 'RadioSet'
treatmentNames<-	Accessing and modifying information in a 'RadioSet'
treatmentNames<--method	Accessing and modifying information in a 'RadioSet'
treatmentResponse	Accessing and modifying information in a 'RadioSet'
treatmentResponse-method	Accessing and modifying information in a 'RadioSet'
treatmentResponse<-	Accessing and modifying information in a 'RadioSet'
treatmentResponse<--method	Accessing and modifying information in a 'RadioSet'

-- U --

updateObject-method

Update the RadioSet class after changes in it struture or API

-- misc --

.RadioSet	A Class to Contain RadioGenomic datasets together with their curations
[-method	'['