1. PharmacoGx
  2. NAMESPACE
Raw Blame Patch Log History 
# Generated by roxygen2: do not edit by hand

S3method(plot,PharmacoSig)
export("drugInfo<-")
export("drugNames<-")
export()
export(.computeAUCUnderFittedCurve)
export(.computeZIPdelta)
export(.deltaScore)
export(.logcosh)
export(.parseToRoxygen)
export(.plotProjHill)
export(PharmacoSet)
export(PharmacoSet2)
export(PharmacoSig)
export(amcc)
export(availablePSets)
export(checkPsetStructure)
export(computeABC)
export(computeAUC)
export(computeAmax)
export(computeBliss)
export(computeHSA)
export(computeIC50)
export(computeICn)
export(computeLoewe)
export(computeSlope)
export(computeZIP)
export(connectivityScore)
export(cosinePerm)
export(downloadPSet)
export(downloadPertSig)
export(drugDoseResponseCurve)
export(drugInfo)
export(drugNames)
export(drugPerturbationSig)
export(effectToDose)
export(estimateProjParams)
export(filterNoisyCurves)
export(fitTwowayZIP)
export(gwc)
export(hillCurve)
export(intersectPSet)
export(loeweCI)
export(logLogisticRegression)
export(mcc)
exportMethods("[")
exportMethods("annotation<-")
exportMethods("curation<-")
exportMethods("datasetType<-")
exportMethods("dateCreated<-")
exportMethods("fNames<-")
exportMethods("featureInfo<-")
exportMethods("mDataNames<-")
exportMethods("molecularProfiles<-")
exportMethods("molecularProfilesSlot<-")
exportMethods("name<-")
exportMethods("pertNumber<-")
exportMethods("phenoInfo<-")
exportMethods("sampleInfo<-")
exportMethods("sampleNames<-")
exportMethods("sensNumber<-")
exportMethods("sensitivityInfo<-")
exportMethods("sensitivityProfiles<-")
exportMethods("sensitivityRaw<-")
exportMethods("treatmentInfo<-")
exportMethods("treatmentNames<-")
exportMethods("treatmentResponse<-")
exportMethods(annotation)
exportMethods(computeZIPdelta)
exportMethods(curation)
exportMethods(datasetType)
exportMethods(dateCreated)
exportMethods(dim)
exportMethods(drugSensitivitySig)
exportMethods(fNames)
exportMethods(featureInfo)
exportMethods(mDataNames)
exportMethods(molecularProfiles)
exportMethods(molecularProfilesSlot)
exportMethods(name)
exportMethods(pertNumber)
exportMethods(phenoInfo)
exportMethods(sampleInfo)
exportMethods(sampleNames)
exportMethods(sensNumber)
exportMethods(sensitivityInfo)
exportMethods(sensitivityMeasures)
exportMethods(sensitivityProfiles)
exportMethods(sensitivityRaw)
exportMethods(show)
exportMethods(showSigAnnot)
exportMethods(subsetByFeature)
exportMethods(subsetBySample)
exportMethods(subsetByTreatment)
exportMethods(subsetTo)
exportMethods(summarizeMolecularProfiles)
exportMethods(summarizeSensitivityProfiles)
exportMethods(treatmentInfo)
exportMethods(treatmentNames)
exportMethods(treatmentResponse)
exportMethods(updateObject)
import(RColorBrewer)
import(caTools)
import(data.table)
import(downloader)
import(ggplot2)
import(jsonlite)
import(methods)
import(parallel)
importClassesFrom(CoreGx,CoreSet)
importClassesFrom(CoreGx,LongTable)
importClassesFrom(CoreGx,TreatmentResponseExperiment)
importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,List)
importFrom(Biobase,AnnotatedDataFrame)
importFrom(BiocParallel,bplapply)
importFrom(CoreGx,"sampleInfo<-")
importFrom(CoreGx,.)
importFrom(CoreGx,.collapse)
importFrom(CoreGx,.dmedncauchys)
importFrom(CoreGx,.dmednnormals)
importFrom(CoreGx,.edmedncauchys)
importFrom(CoreGx,.edmednnormals)
importFrom(CoreGx,.errorMsg)
importFrom(CoreGx,.fitCurve2)
importFrom(CoreGx,.funContext)
importFrom(CoreGx,.getSupportVec)
importFrom(CoreGx,.intersectList)
importFrom(CoreGx,.meshEval)
importFrom(CoreGx,.parseToRoxygen)
importFrom(CoreGx,.reformatData)
importFrom(CoreGx,.residual)
importFrom(CoreGx,.summarizeMolecularNumbers)
importFrom(CoreGx,.warning)
importFrom(CoreGx,CoreSet)
importFrom(CoreGx,CoreSet2)
importFrom(CoreGx,LongTable)
importFrom(CoreGx,TreatmentResponseExperiment)
importFrom(CoreGx,aggregate)
importFrom(CoreGx,buildComboProfiles)
importFrom(CoreGx,idCols)
importFrom(CoreGx,sampleInfo)
importFrom(CoreGx,sampleNames)
importFrom(CoreGx,subsetByFeature)
importFrom(CoreGx,treatmentNames)
importFrom(CoreGx,updateSampleId)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,Assays)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(boot,boot)
importFrom(boot,boot.ci)
importFrom(checkmate,assert)
importFrom(checkmate,assertCharacter)
importFrom(checkmate,assertClass)
importFrom(checkmate,assertDataFrame)
importFrom(checkmate,assertDataTable)
importFrom(checkmate,assertInt)
importFrom(checkmate,assertList)
importFrom(checkmate,assertLogical)
importFrom(checkmate,assertNumeric)
importFrom(checkmate,assertSubset)
importFrom(coop,pcor)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,merge.data.table)
importFrom(data.table,tstrsplit)
importFrom(downloader,download)
importFrom(grDevices,dev.off)
importFrom(grDevices,palette)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(grDevices,rgb)
importFrom(graphics,curve)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,rect)
importFrom(magicaxis,magaxis)
importFrom(methods,callNextMethod)
importFrom(reshape2,acast)
importFrom(stats,anova)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,dcauchy)
importFrom(stats,dnorm)
importFrom(stats,formula)
importFrom(stats,glm)
importFrom(stats,integrate)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,optimise)
importFrom(stats,p.adjust)
importFrom(stats,pcauchy)
importFrom(stats,pf)
importFrom(stats,pnorm)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,quantile)
importFrom(stats,rcauchy)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(utils,combn)
importFrom(utils,read.table)
importFrom(utils,sessionInfo)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
importMethodsFrom(BiocGenerics,"annotation<-")
importMethodsFrom(BiocGenerics,annotation)
importMethodsFrom(CoreGx,"annotation<-")
importMethodsFrom(CoreGx,"curation<-")
importMethodsFrom(CoreGx,"datasetType<-")
importMethodsFrom(CoreGx,"dateCreated<-")
importMethodsFrom(CoreGx,"fNames<-")
importMethodsFrom(CoreGx,"featureInfo<-")
importMethodsFrom(CoreGx,"mDataNames<-")
importMethodsFrom(CoreGx,"molecularProfiles<-")
importMethodsFrom(CoreGx,"molecularProfilesSlot<-")
importMethodsFrom(CoreGx,"name<-")
importMethodsFrom(CoreGx,"pertNumber<-")
importMethodsFrom(CoreGx,"phenoInfo<-")
importMethodsFrom(CoreGx,"sampleNames<-")
importMethodsFrom(CoreGx,"sensNumber<-")
importMethodsFrom(CoreGx,"sensitivityInfo<-")
importMethodsFrom(CoreGx,"sensitivityProfiles<-")
importMethodsFrom(CoreGx,"sensitivityRaw<-")
importMethodsFrom(CoreGx,"treatmentInfo<-")
importMethodsFrom(CoreGx,"treatmentNames<-")
importMethodsFrom(CoreGx,"treatmentResponse<-")
importMethodsFrom(CoreGx,annotation)
importMethodsFrom(CoreGx,curation)
importMethodsFrom(CoreGx,datasetType)
importMethodsFrom(CoreGx,dateCreated)
importMethodsFrom(CoreGx,drugSensitivitySig)
importMethodsFrom(CoreGx,fNames)
importMethodsFrom(CoreGx,featureInfo)
importMethodsFrom(CoreGx,mDataNames)
importMethodsFrom(CoreGx,molecularProfiles)
importMethodsFrom(CoreGx,molecularProfilesSlot)
importMethodsFrom(CoreGx,name)
importMethodsFrom(CoreGx,pertNumber)
importMethodsFrom(CoreGx,phenoInfo)
importMethodsFrom(CoreGx,sampleNames)
importMethodsFrom(CoreGx,sensNumber)
importMethodsFrom(CoreGx,sensitivityInfo)
importMethodsFrom(CoreGx,sensitivityMeasures)
importMethodsFrom(CoreGx,sensitivityProfiles)
importMethodsFrom(CoreGx,sensitivityRaw)
importMethodsFrom(CoreGx,showSigAnnot)
importMethodsFrom(CoreGx,subsetBySample)
importMethodsFrom(CoreGx,subsetByTreatment)
importMethodsFrom(CoreGx,subsetTo)
importMethodsFrom(CoreGx,summarizeMolecularProfiles)
importMethodsFrom(CoreGx,summarizeSensitivityProfiles)
importMethodsFrom(CoreGx,treatmentInfo)
importMethodsFrom(CoreGx,treatmentNames)
importMethodsFrom(CoreGx,treatmentResponse)
importMethodsFrom(CoreGx,updateObject)
useDynLib(PharmacoGx,"_PharmacoGx_partialCorQUICKSTOP")