# Analysis of Large-Scale Radio-Genomic Data

## Documentation for package ‘RadioGx’ version 1.0.0

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

## Help Pages

.RadioSet | A Class to Contain RadioGenomic datasets together with their curations
annotation-method | A Class to Contain RadioGenomic datasets together with their curations
annotation<--method | A Class to Contain RadioGenomic datasets together with their curations
availableRSets | Return a table of RadioSets available for download
cellInfo-method | A Class to Contain RadioGenomic datasets together with their curations
cellInfo<--method | A Class to Contain RadioGenomic datasets together with their curations
cellNames-method | A Class to Contain RadioGenomic datasets together with their curations
cellNames<--method | A Class to Contain RadioGenomic datasets together with their curations
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-method | A Class to Contain RadioGenomic datasets together with their curations
curation<--method | A Class to Contain RadioGenomic datasets together with their curations
datasetType-method | A Class to Contain RadioGenomic datasets together with their curations
datasetType<--method | A Class to Contain RadioGenomic datasets together with their curations
dateCreated-method | A Class to Contain RadioGenomic datasets together with their curations
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
featureInfo-method | A Class to Contain RadioGenomic datasets together with their curations
featureInfo<--method | A Class to Contain RadioGenomic datasets together with their curations
fNames-method | A Class to Contain RadioGenomic datasets together with their curations
fNames<--method | A Class to Contain RadioGenomic datasets together with their curations
linearQuadraticModel | Fit linear-quadratic curves to dose-response data
mDataNames-method | mDataNames
molecularProfiles-method | A Class to Contain RadioGenomic datasets together with their curations
molecularProfiles<--method | A Class to Contain RadioGenomic datasets together with their curations
molecularProfilesSlot-method | A Class to Contain RadioGenomic datasets together with their curations
molecularProfilesSlot<--method | A Class to Contain RadioGenomic datasets together with their curations
name-method | A Class to Contain RadioGenomic datasets together with their curations
pertNumber-method | A Class to Contain RadioGenomic datasets together with their curations
pertNumber<--method | A Class to Contain RadioGenomic datasets together with their curations
phenoInfo-method | A Class to Contain RadioGenomic datasets together with their curations
phenoInfo<--method | A Class to Contain RadioGenomic datasets together with their curations
plotCurve | Plot radiation dose-response curve
radiationInfo | radiationInfo Generic
radiationInfo-method | A Class to Contain RadioGenomic datasets together with their curations
radiationInfo<- | radiationInfo<- Generic
radiationInfo<--method | A Class to Contain RadioGenomic datasets together with their curations
radiationTypes | radiationTypes Generic
radiationTypes-method | A Class to Contain RadioGenomic datasets together with their curations
radiationTypes<- | radiationTypes<- Generic
radiationTypes<--method | A Class to Contain RadioGenomic datasets together with their curations
RadioSet | RadioSet constructor
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.
sensitivityInfo-method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityInfo<--method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityMeasures-method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityProfiles-method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityProfiles<--method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityRaw-method | A Class to Contain RadioGenomic datasets together with their curations
sensitivityRaw<--method | A Class to Contain RadioGenomic datasets together with their curations
sensitivitySlot-method | A Class to Contain RadioGenomic datasets together with their curations
sensitivitySlot<--method | A Class to Contain RadioGenomic datasets together with their curations
sensNumber-method | A Class to Contain RadioGenomic datasets together with their curations
sensNumber<--method | A Class to Contain RadioGenomic datasets together with their curations
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
[-method | '['