.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 | '[' |