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
PharmacoSet-utils       Utility methods for a 'PharmacoSet' object.
PharmacoSet2            Make a CoreSet with the updated class structure
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)
computeBliss            Compute Bliss Null References
computeHSA              Compute HSA Null References
computeIC50             Computes the ICn for any n in 0-100 for a Drug
                        Dose Viability Curve
computeLoewe            Computes Loewe Null References
computeSlope            Return Slope (normalized slope of the drug
                        response curve) for an experiment of a pSet by
                        taking its concentration and viability as
                        input.
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
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).
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.
effectToDose            Inverse function of Hill equation
estimateProjParams      Estimate the projected Hill coefficient,
                        efficacy, and potency
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.
fitTwowayZIP            Two-way fitting for projected dose-response
                        curve.
geneDrugSensitivity     Calcualte The Gene Drug Sensitivity
geneDrugSensitivityPBCorr
                        Calculate The Gene Drug Sensitivity
geneDrugSensitivityPCorr
                        Calculate The Gene Drug Sensitivity
gwc                     GWC Score
hillCurve               4-Parameter Hill Equation for Stimuli-Response
                        Curves
intersectPSet           Intersects objects of the PharmacoSet class,
                        subsetting them to the common drugs and/or cell
                        lines as selected by the user.
loeweCI                 Loewe Additive Combination Index (CI)
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
partialCorQUICKSTOP     QUICKSTOP significance testing for partial
                        correlation
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
updateObject,PharmacoSet-method
                        Update the PharmacoSet class after changes in
                        it struture or API
