Man pages for ToxicoGx
Analysis of Large-Scale Toxico-Genomic Data
| annotation | annotation Slot Getter |
| annotation-set | annotation<- Slot Setter |
| availableTSets | Return a table of ToxicoSets available for download |
| checkTSetStructure | A function to verify the structure of a ToxicoSet |
| computeAUC | Computes the AUC for a Drug Dose Viability Curve |
| computeICn | Computes the ICn for any n in 0-100 for a Drug Dose Viability... |
| computeLimmaDiffExpr | Private getter for .intern environment slot inside an object. |
| computeLimmaDiffExpr-ToxicoSet-method | Conduct differential expression analysis using the limma R... |
| curation | curation Slot Getter |
| curation-set | curation<- Slot Setter |
| datasetType | datasetType Generic |
| datasetType-set | datasetType<- Replacement Generic |
| dim-ToxicoSet-method | Get the dimensions of a ToxicoSet |
| downloadTSet | Download a ToxicoSet object |
| drugGeneResponseCurve | Compares gene expression for a specificed set of features... |
| drugInfo | drugInfo Getter |
| drugInfo-set | drugInfo<- Setter method |
| drugNames | drugNames Generic |
| drugNames-set | drugNames<- Generic |
| drugPerturbationSig | Drug perturbation analysis |
| drugTimeResponseCurve | Compares viabilities at a given dose over different... |
| geneDrugPerturbation | Compute gene-drug associations |
| HCC_sig | HCC_sig dataset |
| logLogisticRegression | Fits curves of the form E = E_inf + (1 - E_inf)/(1 +... |
| mDataNames-ToxicoSet-method | mDataNames |
| name-ToxicoSet-method | name Getter method |
| sensitivityRaw | sensitivityRaw Generic |
| sensitivityRaw-set | sensitivityRaw<- Replacement Generic |
| sensitivitySlot | sensitivitySlot Generic |
| sensitivitySlot-set | sensitivitySlot<- Replacement Generic |
| showSigAnnot | Show the Annotations of a signature object |
| show-ToxicoSet-method | Show a ToxicoSet |
| show-ToxicoSig-method | Show ToxicoGx Signatures |
| subsetTo | A function to subset a ToxicoSet to data containing only... |
| sub-ToxicoSet-ANY-ANY-ANY-method | '[' |
| summarizeMolecularProfiles | Takes molecular data from a ToxicoSet, and summarises them... |
| summarizeSensitivityProfiles | Takes the sensitivity data from a ToxicoSet, and summarises... |
| TGGATESsmall | TGGATESsmall dataset |
| ToxicoSet | ToxicoSet constructor |
| ToxicoSet-class | Class to contain Toxico-genomic Data |
| ToxicoSig | ToxicoSig Constructor |
| updateCellId | A function to update cell ids |
| updateDrugId | A function to update drug ids |
