# Analysis of Large-Scale Toxico-Genomic Data

## Documentation for package ‘ToxicoGx’ version 1.4.0

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

## Help Pages

.ToxicoSet | Class to contain Toxico-genomic Data
annotation | annotation Slot Getter
annotation-method | Class to contain Toxico-genomic Data
annotation<- | annotation<- Slot Setter
annotation<--method | Class to contain Toxico-genomic Data
availableTSets | Return a table of ToxicoSets available for download
cellInfo-method | Class to contain Toxico-genomic Data
cellInfo<--method | Class to contain Toxico-genomic Data
cellNames-method | Class to contain Toxico-genomic Data
cellNames<--method | Class to contain Toxico-genomic Data
checkTSetStructure | A function to verify the structure of a ToxicoSet
computeAUC | Computes the AUC for a Drug Dose Viability Curve
computeIC50 | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeICn | Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve
computeLimmaDiffExpr | Generic method for performing differential expression analysis on an S4 object using the limma package
computeLimmaDiffExpr-method | Conduct differential expression analysis using the limma R pacakge
curation | curation Slot Getter
curation-method | Class to contain Toxico-genomic Data
curation<- | curation<- Slot Setter
curation<--method | Class to contain Toxico-genomic Data
datasetType | datasetType Generic
datasetType-method | Class to contain Toxico-genomic Data
datasetType<- | datasetType<- Replacement Generic
datasetType<--method | Class to contain Toxico-genomic Data
dateCreated-method | Class to contain Toxico-genomic Data
dim-method | Get the dimensions of a ToxicoSet
downloadTSet | Download a ToxicoSet object
drugGeneResponseCurve | Compares gene expression for a specificed set of features over specific drug dosages vs time
drugInfo | drugInfo Getter
drugInfo-method | Class to contain Toxico-genomic Data
drugInfo<- | drugInfo<- Setter method
drugInfo<--method | Class to contain Toxico-genomic Data
drugNames | drugNames Generic
drugNames-method | Class to contain Toxico-genomic Data
drugNames<- | drugNames<- Generic
drugNames<--method | Class to contain Toxico-genomic Data
drugPerturbationSig | Drug perturbation analysis
drugTimeResponseCurve | Compares viabilities at a given dose over different experimental durations
featureInfo-method | Class to contain Toxico-genomic Data
featureInfo<--method | Class to contain Toxico-genomic Data
fNames-method | Class to contain Toxico-genomic Data
fNames<--method | Class to contain Toxico-genomic Data
HCC_sig | HCC_sig dataset
logLogisticRegression | Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.
mDataNames-method | mDataNames
molecularProfiles-method | Class to contain Toxico-genomic Data
molecularProfiles<--method | Class to contain Toxico-genomic Data
molecularProfilesSlot-method | Class to contain Toxico-genomic Data
molecularProfilesSlot<--method | Class to contain Toxico-genomic Data
name-method | name Getter method
pertNumber-method | Class to contain Toxico-genomic Data
pertNumber<--method | Class to contain Toxico-genomic Data
phenoInfo-method | Class to contain Toxico-genomic Data
phenoInfo<--method | Class to contain Toxico-genomic Data
sensitivityInfo-method | Class to contain Toxico-genomic Data
sensitivityInfo<--method | Class to contain Toxico-genomic Data
sensitivityMeasures-method | Class to contain Toxico-genomic Data
sensitivityProfiles-method | Class to contain Toxico-genomic Data
sensitivityProfiles<--method | Class to contain Toxico-genomic Data
sensitivityRaw | sensitivityRaw Generic
sensitivityRaw-method | Class to contain Toxico-genomic Data
sensitivityRaw<- | sensitivityRaw<- Replacement Generic
sensitivityRaw<--method | Class to contain Toxico-genomic Data
sensitivitySlot | sensitivitySlot Generic
sensitivitySlot-method | Class to contain Toxico-genomic Data
sensitivitySlot<- | sensitivitySlot<- Replacement Generic
sensitivitySlot<--method | Class to contain Toxico-genomic Data
sensNumber-method | Class to contain Toxico-genomic Data
sensNumber<--method | Class to contain Toxico-genomic Data
show-method | Show a ToxicoSet
show-method | Show ToxicoGx Signatures
showSigAnnot | Show the Annotations of a signature object
subsetTo | A function to subset a ToxicoSet to data containing only specified drugs, cells and genes
summarizeMolecularProfiles | Takes molecular data from a ToxicoSet, and summarises them into one entry per drug and experimental condition.
summarizeSensitivityProfiles | Takes the sensitivity data from a ToxicoSet, and summarises them into a drug vs cell line table
TGGATESsmall | TGGATESsmall dataset
ToxicoSet | ToxicoSet constructor
ToxicoSet-class | Class to contain Toxico-genomic Data
[-method | '['