Man pages for bhklab/PharmacoGx
Analysis of Large-Scale Pharmacogenomic Data
| amcc | Adaptive Matthews Correlation Coefficient |
| availablePSets | Return a table of PharmacoSets available for download |
| callingWaterfall | Drug sensitivity calling using waterfall plots |
| CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet |
| checkPsetStructure | A function to verify the structure of a PharmacoSet |
| CMAPsmall | Connectivity Map Example PharmacoSet |
| computeABC | Fits dose-response curves to data given by the user and... |
| computeAmax | Fits dose-response curves to data given by the user and... |
| computeAUC | Computes the AUC for a Drug Dose Viability Curve |
| computeBliss | Compute Bliss Null References |
| computeHSA | Compute HSA Null References |
| computeICn | Computes the ICn for any n in 0-100 for a Drug Dose Viability... |
| computeLoewe | Computes Loewe Null References |
| computeSlope | Return Slope (normalized slope of the drug response curve)... |
| computeZIP | Computes ZIP Null References |
| computeZIPdelta | Generic to compute ZIP delta scores from an S4 object |
| computeZIPdelta-TreatmentResponseExperiment-method | Compute ZIP delta score |
| connectivityScore | Function computing connectivity scores between two signatures |
| cosinePerm | Cosine Permuations |
| dim-PharmacoSet-method | Get the dimensions of a PharmacoSet |
| dot-computeZIPdelta | Vector-based version of computeZIPdelta |
| dot-summarizeSensProfiles | Summarize the sensitivity profiles when the sensitivity slot... |
| downloadPertSig | Download Drug Perturbation Signatures |
| downloadPSet | Download a PharmacoSet object |
| drugDoseResponseCurve | Plot drug response curve of a given drug and a given cell for... |
| drugPerturbationSig | Creates a signature representing gene expression (or other... |
| drugSensitivitySig-PharmacoSet-method | Creates a signature representing the association between gene... |
| effectToDose | Inverse function of Hill equation |
| estimateProjParams | Estimate the projected Hill coefficient, efficacy, and... |
| filterNoisyCurves | Viability measurements in dose-reponse curves must remain... |
| fitTwowayZIP | Two-way fitting for projected dose-response curve. |
| GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet |
| geneDrugSensitivity | Calcualte The Gene Drug Sensitivity |
| geneDrugSensitivityPBCorr | Calculate The Gene Drug Sensitivity |
| geneDrugSensitivityPCorr | Calculate The Gene Drug Sensitivity |
| gwc | GWC Score |
| HDAC_genes | HDAC Gene Signature |
| hillCurve | 4-Parameter Hill Equation for Stimuli-Response Curves |
| intersectPSet | Intersects objects of the PharmacoSet class, subsetting them... |
| loeweCI | Loewe Additive Combination Index (CI) |
| logLogisticRegression | Fits curves of the form E = E_inf + (1 - E_inf)/(1 +... |
| mcc | Compute a Mathews Correlation Coefficient |
| partialCorQUICKSTOP | QUICKSTOP significance testing for partial correlation |
| PharmacoSet | PharmacoSet constructor |
| PharmacoSet2 | Make a CoreSet with the updated class structure |
| PharmacoSet-accessors | Accessing and modifying information in a 'PharmacoSet' |
| PharmacoSet-class | A Class to Contain PharmacoGenomic datasets together with... |
| PharmacoSet-utils | Utility methods for a 'PharmacoSet' object. |
| PharmacoSig | Contructor for the PharmacoSig S4 class |
| plot.PharmacoSig | Plots a PharmacoSig object into a Volcano Plot |
| show-PharmacoSet-method | Show a PharamcoSet |
| show-PharmacoSig-method | Show PharmacoGx Signatures |
| showSigAnnot-PharmacoSig-method | Show the Annotations of a signature object |
| sub-PharmacoSet-ANY-ANY-ANY-method | '[' |
| subsetTo-PharmacoSet-method | A function to subset a PharmacoSet to data containing only... |
| summarizeMolecularProfiles-PharmacoSet-method | Takes molecular data from a PharmacoSet, and summarises them... |
| summarizeSensitivityProfiles-PharmacoSet-method | Takes the sensitivity data from a PharmacoSet, and summarises... |
| updateObject-PharmacoSet-method | Update the PharmacoSet class after changes in it struture or... |
