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| .PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations |
| 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 |
| cellInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| cellInfo<--method | cellInfo<- Generic |
| cellNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| cellNames<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| 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 returns the ABC of the fitted curves. |
| computeAmax | Fits dose-response curves to data given by the user and returns the Amax of the fitted curve. Amax: 100 - viability at maximum concentarion (in fitted curve) |
| 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 |
| computeSlope | Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input. |
| connectivityScore | Function computing connectivity scores between two signatures |
| cosinePerm | Cosine Permuations |
| dateCreated-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| dim-method | Get the dimensions of a PharmacoSet |
| downloadPertSig | Download Drug Perturbation Signatures |
| downloadPSet | Download a PharmacoSet object |
| drugDoseResponseCurve | Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class). |
| drugInfo | drugInfo Generic |
| drugInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| drugInfo<- | drugInfo<- Generic |
| drugInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| drugNames | drugNames Generic |
| drugNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| drugNames<- | drugNames<- Generic |
| drugNames<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| drugPerturbationSig | Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis. |
| drugSensitivitySig-method | Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis. |
| featureInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| featureInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| filterNoisyCurves | Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions. |
| fNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| fNames<--method | fNames<- |
| GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet |
| geneDrugSensitivity | Calcualte The Gene Drug Sensitivity |
| gwc | GWC Score |
| HDAC_genes | HDAC Gene Signature |
| intersectPSet | Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user. |
| 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. |
| mcc | Compute a Mathews Correlation Coefficient |
| mDataNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| molecularProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| molecularProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| molecularProfilesSlot-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| molecularProfilesSlot<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| name-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| name<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| pertNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| pertNumber<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| PharmacoSet | PharmacoSet constructor |
| PharmacoSet-class | A Class to Contain PharmacoGenomic datasets together with their curations |
| PharmacoSig | Contructor for the PharmacoSig S4 class |
| phenoInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| phenoInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| plot.PharmacoSig | Plots a PharmacoSig object into a Volcano Plot |
| sensitivityInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityMeasures-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityMeasures<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityRaw-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityRaw<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivitySlot-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivitySlot<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivitySlotToLongTable-method | Reconstruct the data in the @sensitivity slot list into a LongTable object. |
| sensNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensNumber<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| show-method | Show a PharamcoSet |
| show-method | Show PharmacoGx Signatures |
| showSigAnnot-method | Show the Annotations of a signature object |
| subsetTo-method | A function to subset a PharmacoSet to data containing only specified drugs, cells and genes |
| summarizeSensitivityProfiles-method | Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table |
| [-method | '[' |