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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
drugInfo() `drugInfo<-`() drugNames() `drugNames<-`() annotation(<PharmacoSet> ) `annotation<-`(<PharmacoSet> ,<list> ) dateCreated(<PharmacoSet> ) `dateCreated<-`(<PharmacoSet> ,<character> ) name(<PharmacoSet> ) `name<-`(<PharmacoSet> ) sampleInfo(<PharmacoSet> ) `sampleInfo<-`(<PharmacoSet> ,<data.frame> ) sampleNames(<PharmacoSet> ) `sampleNames<-`(<PharmacoSet> ,<character> ) curation(<PharmacoSet> ) `curation<-`(<PharmacoSet> ,<list> ) datasetType(<PharmacoSet> ) `datasetType<-`(<PharmacoSet> ,<character> ) molecularProfiles(<PharmacoSet> ) `molecularProfiles<-`(<PharmacoSet> ,<character> ,<character> ,<matrix> ) featureInfo(<PharmacoSet> ) `featureInfo<-`(<PharmacoSet> ,<character> ,<data.frame> ) phenoInfo(<PharmacoSet> ,<character> ) `phenoInfo<-`(<PharmacoSet> ,<character> ,<data.frame> ) fNames(<PharmacoSet> ,<character> ) `fNames<-`(<PharmacoSet> ,<character> ,<character> ) mDataNames(<PharmacoSet> ) `mDataNames<-`(<PharmacoSet> ) molecularProfilesSlot(<PharmacoSet> ) `molecularProfilesSlot<-`(<PharmacoSet> ,<list_OR_MAE> ) sensitivityInfo(<PharmacoSet> ) `sensitivityInfo<-`(<PharmacoSet> ,<data.frame> ) sensitivityMeasures(<PharmacoSet> ) `sensitivityMeasures<-`(<PharmacoSet> ,<character> ) sensitivityProfiles(<PharmacoSet> ) `sensitivityProfiles<-`(<PharmacoSet> ,<data.frame> ) sensitivityRaw(<PharmacoSet> ) `sensitivityRaw<-`(<PharmacoSet> ,<array> ) treatmentResponse(<PharmacoSet> ) `treatmentResponse<-`(<PharmacoSet> ,<list_OR_LongTable> ) sensNumber(<PharmacoSet> ) `sensNumber<-`(<PharmacoSet> ,<matrix> ) pertNumber(<PharmacoSet> ) `pertNumber<-`(<PharmacoSet> ,<array> )
Accessing and modifying information in a PharmacoSet
PharmacoSet-class .PharmacoSet
A Class to Contain PharmacoGenomic datasets together with their curations
subsetBySample(<PharmacoSet> ) subsetByTreatment(<PharmacoSet> ) subsetByFeature(<PharmacoSet> )
Utility methods for a PharmacoSet object.
PharmacoSet()
PharmacoSet constructor
PharmacoSet2()
Make a CoreSet with the updated class structure
PharmacoSig()
Contructor for the PharmacoSig S4 class
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() computeICn()
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(<TreatmentResponseExperiment> )
Compute ZIP delta score
computeZIPdelta()
Generic to compute ZIP delta scores from an S4 object
connectivityScore()
Function computing connectivity scores between two signatures
cosinePerm()
Cosine Permuations
dim(<PharmacoSet> )
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> )
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> )
Show a PharamcoSet
show(<PharmacoSig> )
Show PharmacoGx Signatures
showSigAnnot(<PharmacoSig> )
Show the Annotations of a signature object
`[`(<PharmacoSet> ,<ANY> ,<ANY> ,<ANY> )
[
subsetTo(<PharmacoSet> )
A function to subset a PharmacoSet to data containing only specified drugs, cells and genes
summarizeSensitivityProfiles(<PharmacoSet> )
Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table
updateObject(<PharmacoSet> )
Update the PharmacoSet class after changes in it struture or API