CCLEsmall               Cancer Cell Line Encyclopedia (CCLE) Example
                        PharmacoSet
CMAPsmall               Connectivity Map Example PharmacoSet
GDSCsmall               Genomics of Drug Sensitivity in Cancer Example
                        PharmacoSet
HDAC_genes              HDAC Gene Signature
PharmacoSet             PharmacoSet constructor
PharmacoSet-class       A Class to Contain PharmacoGenomic datasets
                        together with their curations
[,PharmacoSet,ANY,ANY,ANY-method
                        '['
amcc                    Calculate an Adaptive Matthews Correlation
                        Coefficient
availablePSets          Return a table of PharmacoSets available for
                        download
cellInfo                cellInfo Generic
cellInfo<-              cellInfo<- Generic
cellNames               cellNames Generic
cellNames<-             cellNames<- Generic
checkPSetStructure      A function to verify the structure of a
                        PharmacoSet
computeABC              Fits dose-response curves to data given by the
                        user and returns the ABC of the fitted curves.
computeAUC              Computes the AUC for a Drug Dose Viability
                        Curve
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)
computeIC50             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
dim,PharmacoSet-method
                        Get the dimensions of a PharmacoSet
downloadPSet            Download a PharmacoSet object
downloadPertSig         Download Drug Perturbation Signatures
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<-              drugInfo<- Generic
drugNames               drugNames Generic
drugNames<-             drugNames<- Generic
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.
fNames                  fNames Generic
featureInfo             featureInfo Generic
featureInfo<-           featureInfo<- Generic
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.
gwc                     Calculate the gwc score between two vectors,
                        using either a weighted spearman or pearson
                        correlation
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.
mDataNames              mDataNames
mcc                     Compute a Mathews Correlation Coefficient
molecularProfiles       molecularProfiles Generic
molecularProfiles<-     molecularProfiles<- Generic
pSetName                pSetName Generic
pertNumber              pertNumber Generic
pertNumber<-            pertNumber<- Generic
phenoInfo               phenoInfo Generic
phenoInfo<-             phenoInfo<- Generic
sensNumber              sensNumber Generic
sensNumber<-            sensNumber<- Generic
sensitivityInfo         sensitivityInfo Generic
sensitivityInfo<-       sensitivityInfo<- Generic
sensitivityMeasures     sensitivityMeasures Generic
sensitivityProfiles     sensitivityProfiles Generic
sensitivityProfiles<-   sensitivityProfiles<- Generic
show,PharmacoSet-method
                        Show a PharamcoSet
show,PharmacoSig-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
symSetDiffList          Utility to find the symmetric set difference of
                        a list of two or more vectors or lists
unionList               Utility to find the union between a list of
                        more than two vectors or lists
