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-accessors   Accessing and modifying information in a
                        'PharmacoSet'
PharmacoSet-class       A Class to Contain PharmacoGenomic datasets
                        together with their curations
PharmacoSig             Contructor for the PharmacoSig S4 class
[,PharmacoSet,ANY,ANY,ANY-method
                        '['
amcc                    Adaptive Matthews Correlation Coefficient
availablePSets          Return a table of PharmacoSets available for
                        download
callingWaterfall        Drug sensitivity calling using waterfall plots
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              Cosine Permuations
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,PharmacoSet-method
                        Creates a signature representing the
                        association between gene expression (or other
                        molecular profile) and drug dose response, for
                        use in drug sensitivity analysis.
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.
geneDrugSensitivity     Calcualte The Gene Drug Sensitivity
gwc                     GWC Score
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
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
subsetTo,PharmacoSet-method
                        A function to subset a PharmacoSet to data
                        containing only specified drugs, cells and
                        genes
summarizeSensitivityProfiles,PharmacoSet-method
                        Takes the sensitivity data from a PharmacoSet,
                        and summarises them into a drug vs cell line
                        table
