Analysis of Large-Scale Toxico-Genomic Data

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Documentation for package ‘ToxicoGx’ version 1.0.1

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.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-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 '['