{"id":"survivalAnalysis","name":"Survival Analysis","dataTypes":{"subset1":["CLINICAL.TXT"]},"dataFileInputMapping":{"CLINICAL.TXT":"TRUE","SNP.TXT":"snpData","MRNA_DETAILED.TXT":"mrnaData"},"pivotData":false,"variableMapping":{"||SNPTYPEDEP||":"divDependentVariableSNPType","||BINNING||":"binning","||GPLDEP||":"divDependentVariablegpls","||GENESDEPNAME||":"divDependentPathwayName","||NUMBERBINS||":"numberOfBins","||BINNINGTYPE||":"binDistribution","||PLATFORMDEP||":"divDependentVariableplatforms","||TISSUEDEP||":"divDependentVariabletissues","||CATEGORY||":"categoryVariable","||GENESDEP||":"divDependentVariablePathway","||AGGREGATEDEP||":"divDependentVariableprobesAggregation","||TIMEPOINTSDEP||":"divDependentVariabletimepoints","||BINNINGRANGESTRING||":"binRanges","||BINNINGVARIABLETYPE||":"variableType","||RBMPANELDEP||":"divDependentVariablerbmPanels","||TIME||":"timeVariable","||SAMPLEDEP||":"divDependentVariablesamples","||TYPEDEP||":"divDependentVariableType","||EVENTYES||":"censoringVariable","||BINNINGMANUAL||":"manualBinning","||GPLCAT||":"divDependentVariablegpls"},"converter":{"R":["source('||PLUGINSCRIPTDIRECTORY||Common/dataBuilders.R')","source('||PLUGINSCRIPTDIRECTORY||Common/ExtractConcepts.R')","source('||PLUGINSCRIPTDIRECTORY||Common/collapsingData.R')","source('||PLUGINSCRIPTDIRECTORY||Common/BinData.R')","source('||PLUGINSCRIPTDIRECTORY||Survival/BuildSurvivalData.R')","SurvivalData.build(\n        input.dataFile           = '||TEMPFOLDERDIRECTORY||Clinical/clinical.i2b2trans',\n        concept.time             = '||TIME||',\n        concept.category         = '||CATEGORY||',\n        concept.eventYes         = '||EVENTYES||',\n        binning.enabled          = '||BINNING||',\n        binning.bins             = '||NUMBERBINS||',\n        binning.type             = '||BINNINGTYPE||',\n        binning.manual           = '||BINNINGMANUAL||',\n        binning.binrangestring   = '||BINNINGRANGESTRING||',\n        binning.variabletype     = '||BINNINGVARIABLETYPE||',\n        input.gexFile            = '||TEMPFOLDERDIRECTORY||mRNA/Processed_Data/mRNA.trans',\n        input.snpFile            = '||TEMPFOLDERDIRECTORY||SNP/snp.trans',\n        concept.category.type    = '||TYPEDEP||',\n        genes.category           = '||GENESDEP||',\n        genes.category.aggregate = '||AGGREGATEDEP||',\n        sample.category          = '||SAMPLEDEP||',\n        time.category            = '||TIMEPOINTSDEP||',\n        snptype.category         = '||SNPTYPEDEP||',\n        gpl.category             = '||GPLCAT||')"]},"processor":{"R":["source('||PLUGINSCRIPTDIRECTORY||Survival/CoxRegressionLoader.r')","CoxRegression.loader(input.filename='outputfile')","source('||PLUGINSCRIPTDIRECTORY||Survival/SurvivalCurveLoader.r')","SurvivalCurve.loader(input.filename='outputfile',concept.time='||TIME||')"]},"renderer":{"GSP":"/survivalAnalysis/survivalAnalysisOutput"},"view":"SurvivalAnalysis"}