API for bhklab/PharmacoGx
Analysis of Large-Scale Pharmacogenomic Data

Global functions
.GR	Source code
.Hill	Source code
.PharmacoSet	Man page
.calculateFromRaw	Source code
.computeAUCUnderFittedCurve	Source code
.computeCumSumDelta	Source code
.computeDelta	Source code
.computeZIPdelta	Man page Source code
.createPSetEntry	Source code
.deltaScore	Source code
.drugSensitivitySigPharmacoSet	Source code
.fitProjParamsLoss	Source code
.getCommonConcentrationRange	Source code
.loeweLoss	Source code
.logcosh	Source code
.logcoshLoss	Source code
.meshEval	Source code
.onAttach	Source code
.onLoad	Source code
.optimizeRegression	Source code
.parseToRoxygen	Source code
.plotProjHill	Source code
.rescale	Source code
.residual	Source code
.showSigAnnotPharmacoSig	Source code
.subsetToPharmacoSet	Source code
.summarizeMolecularNumbers	Source code
.summarizePerturbationNumbers	Source code
.summarizeSensProfiles	Man page Source code
.summarizeSensitivityNumbers	Source code
.summarizeSensitivityProfilesPharmacoSet	Source code
CCLEsmall	Man page
CMAPsmall	Man page
GDSCsmall	Man page
HDAC_genes	Man page
PharmacoSet	Man page Source code
PharmacoSet-accessors	Man page
PharmacoSet-class	Man page
PharmacoSet-utils	Man page
PharmacoSet2	Man page Source code
PharmacoSig	Man page Source code
[,PharmacoSet,ANY,ANY,ANY-method	Man page
`drugInfo<-`	Source code
`drugNames<-`	Source code
amcc	Man page Source code
annotation	Man page
annotation,PharmacoSet-method	Man page
annotation<-	Man page
annotation<-,PharmacoSet,list-method	Man page
availablePSets	Man page Source code
callingWaterfall	Man page Source code
cellInfo	Man page
cellInfo,PharmacoSet-method	Man page
cellInfo<-	Man page
cellInfo<-,PharmacoSet,data.frame-method	Man page
cellName,PharmacoSet-method	Man page
cellNames	Man page
cellNames<-	Man page
cellNames<-,PharmacoSet,list-method	Man page
checkPsetStructure	Man page Source code
computeABC	Man page Source code
computeAUC	Man page
computeAUC_old	Source code
computeAmax	Man page Source code
computeBliss	Man page Source code
computeDSS	Source code
computeHSA	Man page Source code
computeIC50	Man page Source code
computeICn	Man page Source code
computeLoewe	Man page Source code
computeSlope	Man page Source code
computeZIP	Man page Source code
computeZIPdelta	Man page
computeZIPdelta,TreatmentResponseExperiment-method	Man page
connectivityScore	Man page Source code
cor.boot	Source code Source code
corPermute	Source code
cosinePerm	Man page Source code
curation	Man page
curation,PharmacoSet-method	Man page
curation<-	Man page
curation<-,PharmacoSet,list-method	Man page
datasetType	Man page
datasetType,PharmacoSet-method	Man page
datasetType<-	Man page
datasetType<-,PharmacoSet,character-method	Man page
dateCreated	Man page
dateCreated,PharmacoSet-method	Man page
dateCreated<-	Man page
dateCreated<-,PharmacoSet,character-method	Man page
dateCreated<-,PharmacoSet-method	Man page
dim,PharmacoSet-method	Man page
downloadPSet	Man page Source code
downloadPertSig	Man page Source code
drugDoseResponseCurve	Man page Source code
drugInfo	Man page Source code
drugInfo<-	Man page
drugNames	Man page Source code
drugNames<-	Man page
drugPerturbationSig	Man page Source code
drugSensitivitySig,PharmacoSet-method	Man page
effectToDose	Man page Source code
estimateProjParams	Man page Source code
fNames	Man page
fNames,PharmacoSet,character-method	Man page
fNames<-	Man page
fNames<-,PharmacoSet,character,character-method	Man page
featureInfo	Man page
featureInfo,PharmacoSet-method	Man page
featureInfo<-	Man page
featureInfo<-,PharmacoSet,character,DataFrame-method	Man page
featureInfo<-,PharmacoSet,character,data.frame-method	Man page
filterNoisyCurves	Man page Source code
fitTwowayZIP	Man page Source code
geneDrugPerturbation	Source code
geneDrugSensitivity	Man page Source code
geneDrugSensitivityPBCorr	Man page Source code
geneDrugSensitivityPCorr	Man page Source code
getRawSensitivityMatrix	Source code
grRegression	Source code
gwc	Man page
hillCurve	Man page Source code
intersectPSet	Man page Source code
loeweCI	Man page Source code
logLogisticRegression	Man page Source code
log_denom	Source code Source code
mDataNames	Man page
mDataNames,PharmacoSet-method	Man page
mDataNames<-	Man page
mDataNames<-,PharmacoSet,ANY-method	Man page
mDataNames<-,PharmacoSet-method	Man page
mcc	Man page Source code
mergePSets	Source code
molecularProfiles	Man page
molecularProfiles,PharmacoSet-method	Man page
molecularProfiles<-	Man page
molecularProfiles<-,PharmacoSet,character,character,matrix-metho	Man page
molecularProfiles<-,PharmacoSet,character,missing,matrix-method	Man page
molecularProfiles<-,PharmacoSet,missing,missing,MutliAssayExperi	Man page
molecularProfiles<-,PharmacoSet,missing,missing,list-method	Man page
molecularProfilesSlot	Man page
molecularProfilesSlot,PharmacoSet-method	Man page
molecularProfilesSlot<-	Man page
molecularProfilesSlot<-,PharmacoSet,list-method	Man page
molecularProfilesSlot<-,PharmacoSet,list_OR_MAE-method	Man page
molecularProfilesSlot<-PharmacoSet,MultiAssayExperiment-method	Man page
moleculerProfilesSlot,PharmacoSet-method	Man page
name	Man page
name,PharmacoSet-method	Man page
name<-	Man page
name<-,PharmacoSet,character-method	Man page
name<-,PharmacoSet-method	Man page
partialCorQUICKSTOP	Man page Source code
pertNumber	Man page
pertNumber,PharmacoSet-method	Man page
pertNumber<-	Man page
pertNumber<-,PharmacoSet,array-method	Man page
phenoInfo	Man page
phenoInfo,PharmacoSet,character-method	Man page
phenoInfo<-	Man page
phenoInfo<-,PharmacoSet,character,DataFrame-method	Man page
phenoInfo<-,PharmacoSet,character,data.frame-method	Man page
plot.PharmacoSig	Man page Source code
sampleInfo	Man page
sampleInfo,PharmacoSet-method	Man page
sampleInfo<-	Man page
sampleInfo<-,PharmacoSet,data.frame-method	Man page
sampleName,PharmacoSet-method	Man page
sampleNames	Man page
sampleNames,PharmacoSet-method	Man page
sampleNames<-	Man page
sampleNames<-,PharmacoSet,character-method	Man page
sampleNames<-,PharmacoSet,list-method	Man page
sanitizeInput	Source code
sensNumber	Man page
sensNumber,PharmacoSet-method	Man page
sensNumber<-	Man page
sensNumber<-,PharmacoSet,matrix-method	Man page
sensitivityInfo,PharmacoSet,character-method	Man page
sensitivityInfo,PharmacoSet,missing-method	Man page
sensitivityInfo,PharmacoSet-method	Man page
sensitivityInfo<-,PharmacoSet,data.frame-method	Man page
sensitivityInfo<-,PharmacoSet,missing,data.frame-method	Man page
sensitivityMeasures,PharmacoSet-method	Man page
sensitivityMeasures<-,PharmacoSet,character-method	Man page
sensitivityProfiles,PharmacoSet-method	Man page
sensitivityProfiles<-,PharmacoSet,data.frame-method	Man page
sensitivityRaw,PharmacoSet-method	Man page
sensitivityRaw<-,PharmacoSet,array-method	Man page
sensitivitySlot	Man page
sensitivitySlot<-	Man page
sensitvityInfo<-,PharmacoSet,character,data.frame-method	Man page
show,PharmacoSet-method	Man page
show,PharmacoSig-method	Man page
showSigAnnot,PharmacoSig-method	Man page
subsetByFeature	Man page
subsetByFeature,PharmacoSet-method	Man page
subsetBySample	Man page
subsetBySample,CoreSet-method	Man page
subsetBySample,PharmacoSet-method	Man page
subsetByTreatment	Man page
subsetByTreatment,PharmacoSet-method	Man page
subsetTo,PharmacoSet-method	Man page
summarizeMolecularProfiles,PharmacoSet-method	Man page
summarizeSensitivityProfiles,PharmacoSet-method	Man page
treamentResponse<-,PharmacoSet,list-method	Man page
treatmentInfo	Man page
treatmentInfo,PharmacoSet-method	Man page
treatmentInfo<-	Man page
treatmentInfo<-,PharmacoSet,data.frame-method	Man page
treatmentNames	Man page
treatmentNames,PharmacoSet-method	Man page
treatmentNames<-	Man page
treatmentNames<-,PharmacoSet,character-method	Man page
treatmentResponse	Man page
treatmentResponse,PharmacoSet-method	Man page
treatmentResponse<-	Man page
treatmentResponse<-,PharmacoSet,LongTable-method	Man page
treatmentResponse<-,PharmacoSet,list_OR_LongTable-method	Man page
updateCellId	Source code
updateMaxConc	Source code
updateObject,PharmacoSet-method	Man page