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| .PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations |
| amcc | Calculate an Adaptive Matthews Correlation Coefficient |
| availablePSets | Return a table of PharmacoSets available for download |
| CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet |
| cellInfo | cellInfo Generic |
| cellInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| cellInfo<- | cellInfo<- Generic |
| cellInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| cellNames | cellNames Generic |
| cellNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| cellNames<- | cellNames<- Generic |
| 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 | Computes the cosine similarity and significance using permutation test |
| dateCreated | dateCreated Generic |
| 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 | Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis. |
| featureInfo | featureInfo Generic |
| featureInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| featureInfo<- | featureInfo<- Generic |
| featureInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| fNames | fNames Generic |
| fNames-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet |
| gwc | Calculate the gwc score between two vectors, using either a weighted spearman or pearson correlation |
| HDAC_genes | HDAC Gene Signature |
| intersectList | Utility to find the intersection between a list of more than two vectors or lists |
| 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 | mDataNames |
| molecularProfiles | molecularProfiles Generic |
| molecularProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| molecularProfiles<- | molecularProfiles<- Generic |
| molecularProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| pertNumber | pertNumber Generic |
| pertNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| pertNumber<- | pertNumber<- Generic |
| 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 |
| phenoInfo | phenoInfo Generic |
| phenoInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| phenoInfo<- | phenoInfo<- Generic |
| phenoInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| pSetName | pSetName Generic |
| pSetName-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityInfo | sensitivityInfo Generic |
| sensitivityInfo-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityInfo<- | sensitivityInfo<- Generic |
| sensitivityInfo<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityMeasures | sensitivityMeasures Generic |
| sensitivityMeasures-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityProfiles | sensitivityProfiles Generic |
| sensitivityProfiles-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensitivityProfiles<- | sensitivityProfiles<- Generic |
| sensitivityProfiles<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensNumber | sensNumber Generic |
| sensNumber-method | A Class to Contain PharmacoGenomic datasets together with their curations |
| sensNumber<- | sensNumber<- Generic |
| sensNumber<--method | A Class to Contain PharmacoGenomic datasets together with their curations |
| show-method | Show a PharamcoSet |
| show-method | Show PharmacoGx Signatures |
| showSigAnnot | Show the Annotations of a signature object |
| subsetTo | A function to subset a PharmacoSet to data containing only specified drugs, cells and genes |
| summarizeMolecularProfiles | Takes molecular data from a PharmacoSet, and summarises them into one entry per drug |
| summarizeSensitivityProfiles | Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table |
| unionList | Utility to find the union between a list of more than two vectors or lists |
| [-method | '[' |