| annotation | Accessing and modifying information in a 'CoreSet' |
| annotation-method | Accessing and modifying information in a 'CoreSet' |
| annotation<- | Accessing and modifying information in a 'CoreSet' |
| annotation<--method | Accessing and modifying information in a 'CoreSet' |
| availableTSets | Return a table of ToxicoSets available for download |
| cellInfo | Accessing and modifying information in a 'CoreSet' |
| cellInfo-method | Accessing and modifying information in a 'CoreSet' |
| cellInfo<- | Accessing and modifying information in a 'CoreSet' |
| cellInfo<--method | Accessing and modifying information in a 'CoreSet' |
| cellName-method | Accessing and modifying information in a 'CoreSet' |
| cellNames | Accessing and modifying information in a 'CoreSet' |
| cellNames<- | Accessing and modifying information in a 'CoreSet' |
| cellNames<--method | Accessing and modifying information in a 'CoreSet' |
| 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 | Accessing and modifying information in a 'CoreSet' |
| curation-method | Accessing and modifying information in a 'CoreSet' |
| curation<- | Accessing and modifying information in a 'CoreSet' |
| curation<--method | Accessing and modifying information in a 'CoreSet' |
| datasetType | Accessing and modifying information in a 'CoreSet' |
| datasetType-method | Accessing and modifying information in a 'CoreSet' |
| datasetType<- | Accessing and modifying information in a 'CoreSet' |
| datasetType<--method | Accessing and modifying information in a 'CoreSet' |
| dateCreated | Accessing and modifying information in a 'CoreSet' |
| dateCreated-method | Accessing and modifying information in a 'CoreSet' |
| dateCreated<- | Accessing and modifying information in a 'CoreSet' |
| dateCreated<--method | Accessing and modifying information in a 'CoreSet' |
| 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 | Accessing and modifying information in a 'CoreSet' |
| drugInfo<- | Accessing and modifying information in a 'CoreSet' |
| drugNames | Accessing and modifying information in a 'CoreSet' |
| drugNames<- | Accessing and modifying information in a 'CoreSet' |
| drugPerturbationSig | Drug perturbation analysis |
| drugTimeResponseCurve | Compares viabilities at a given dose over different experimental durations |
| featureInfo | Accessing and modifying information in a 'CoreSet' |
| featureInfo-method | Accessing and modifying information in a 'CoreSet' |
| featureInfo<- | Accessing and modifying information in a 'CoreSet' |
| featureInfo<--method | Accessing and modifying information in a 'CoreSet' |
| fNames | Accessing and modifying information in a 'CoreSet' |
| fNames-method | Accessing and modifying information in a 'CoreSet' |
| fNames<- | Accessing and modifying information in a 'CoreSet' |
| fNames<--method | Accessing and modifying information in a 'CoreSet' |
| 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 | Accessing and modifying information in a 'CoreSet' |
| mDataNames-method | Accessing and modifying information in a 'CoreSet' |
| mDataNames<- | Accessing and modifying information in a 'CoreSet' |
| mDataNames<--method | Accessing and modifying information in a 'CoreSet' |
| molecularProfiles | Accessing and modifying information in a 'CoreSet' |
| molecularProfiles-method | Accessing and modifying information in a 'CoreSet' |
| molecularProfiles<- | Accessing and modifying information in a 'CoreSet' |
| molecularProfiles<--method | Accessing and modifying information in a 'CoreSet' |
| molecularProfilesSlot | Accessing and modifying information in a 'CoreSet' |
| molecularProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
| molecularProfilesSlot<- | Accessing and modifying information in a 'CoreSet' |
| molecularProfilesSlot<--method | Accessing and modifying information in a 'CoreSet' |
| molecularProfilesSlot<-ToxicoSet-method | Accessing and modifying information in a 'CoreSet' |
| moleculerProfilesSlot-method | Accessing and modifying information in a 'CoreSet' |
| name | Accessing and modifying information in a 'CoreSet' |
| name-method | Accessing and modifying information in a 'CoreSet' |
| name<- | Accessing and modifying information in a 'CoreSet' |
| name<--method | Accessing and modifying information in a 'CoreSet' |
| pertNumber | Accessing and modifying information in a 'CoreSet' |
| pertNumber-method | Accessing and modifying information in a 'CoreSet' |
| pertNumber<- | Accessing and modifying information in a 'CoreSet' |
| pertNumber<--method | Accessing and modifying information in a 'CoreSet' |
| phenoInfo | Accessing and modifying information in a 'CoreSet' |
| phenoInfo-method | Accessing and modifying information in a 'CoreSet' |
| phenoInfo<- | Accessing and modifying information in a 'CoreSet' |
| phenoInfo<--method | Accessing and modifying information in a 'CoreSet' |
| sampleInfo | Accessing and modifying information in a 'CoreSet' |
| sampleInfo-method | Accessing and modifying information in a 'CoreSet' |
| sampleInfo<- | Accessing and modifying information in a 'CoreSet' |
| sampleInfo<--method | Accessing and modifying information in a 'CoreSet' |
| sampleName-method | Accessing and modifying information in a 'CoreSet' |
| sampleNames | Accessing and modifying information in a 'CoreSet' |
| sampleNames-method | Accessing and modifying information in a 'CoreSet' |
| sampleNames<- | Accessing and modifying information in a 'CoreSet' |
| sampleNames<--method | Accessing and modifying information in a 'CoreSet' |
| sensitivityInfo-method | Accessing and modifying information in a 'CoreSet' |
| sensitivityInfo<--method | Accessing and modifying information in a 'CoreSet' |
| sensitivityMeasures-method | Accessing and modifying information in a 'CoreSet' |
| sensitivityMeasures<--method | Accessing and modifying information in a 'CoreSet' |
| sensitivityProfiles-method | Accessing and modifying information in a 'CoreSet' |
| sensitivityProfiles<--method | Accessing and modifying information in a 'CoreSet' |
| sensitivityRaw-method | Accessing and modifying information in a 'CoreSet' |
| sensitivityRaw<--method | Accessing and modifying information in a 'CoreSet' |
| sensitivitySlot | Accessing and modifying information in a 'CoreSet' |
| sensitivitySlot<- | Accessing and modifying information in a 'CoreSet' |
| sensitvityInfo<--method | Accessing and modifying information in a 'CoreSet' |
| sensNumber | Accessing and modifying information in a 'CoreSet' |
| sensNumber-method | Accessing and modifying information in a 'CoreSet' |
| sensNumber<- | Accessing and modifying information in a 'CoreSet' |
| sensNumber<--method | Accessing and modifying information in a 'CoreSet' |
| 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-accessors | Accessing and modifying information in a 'CoreSet' |
| ToxicoSet-class | Class to contain Toxico-genomic Data |
| treamentResponse<--method | Accessing and modifying information in a 'CoreSet' |
| treatmentInfo | Accessing and modifying information in a 'CoreSet' |
| treatmentInfo-method | Accessing and modifying information in a 'CoreSet' |
| treatmentInfo<- | Accessing and modifying information in a 'CoreSet' |
| treatmentInfo<--method | Accessing and modifying information in a 'CoreSet' |
| treatmentNames | Accessing and modifying information in a 'CoreSet' |
| treatmentNames-method | Accessing and modifying information in a 'CoreSet' |
| treatmentNames<- | Accessing and modifying information in a 'CoreSet' |
| treatmentNames<--method | Accessing and modifying information in a 'CoreSet' |
| treatmentResponse | Accessing and modifying information in a 'CoreSet' |
| treatmentResponse-method | Accessing and modifying information in a 'CoreSet' |
| treatmentResponse<- | Accessing and modifying information in a 'CoreSet' |
| treatmentResponse<--method | Accessing and modifying information in a 'CoreSet' |
| updateObject-method | Update the ToxicoSet class after changes in it struture or API |
| .ToxicoSet | Class to contain Toxico-genomic Data |
| [-method | '[' |