# Analysis of Large-Scale Radio-Genomic Data

## Documentation for package ‘RadioGx’ version 2.8.0

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

## Help Pages

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 | '['