{"id":"aCGHSurvivalAnalysis","name":"aCGH Survival Analysis","dataTypes":{"subset1":["CLINICAL.TXT"]},"dataFileInputMapping":{"CLINICAL.TXT":"TRUE","ACGH_REGIONS.TXT":"TRUE"},"pivotData":false,"variableMapping":{"||REGION||":"regionVariable","||TIME||":"timeVariable","||EVENTNO||":"censoringVariable","||ABERRATIONTYPE||":"aberrationType","||CONFIDENCEINTERVALS||":"confidenceIntervals"},"converter":{"R":["source('||PLUGINSCRIPTDIRECTORY||aCGH/aCGHBuildSurvivalData.R')","aCGHSurvivalData.build(\n\tinput.dataFile  = '||TEMPFOLDERDIRECTORY||Clinical/clinical.i2b2trans',\n\tinput.acghFile  = '||TEMPFOLDERDIRECTORY||aCGH/regions.txt',\n\tconcept.time    = '||TIME||',\n\tconcept.region  = '||REGION||',\n\tconcept.eventNo = '||EVENTNO||',\n\toutput.survival = 'Overall survival time',\n\toutput.status   = 'Survival status',\n\toutput.dataFile = 'phenodata.tsv',\n\toutput.acghFile = 'regions.tsv')"]},"processor":{"R":["source('||PLUGINSCRIPTDIRECTORY||aCGH/acgh-survival-test.R')","acgh.survival.test(\n\tsurvival               = 'Overall survival time',\n\tstatus                 = 'Survival status',\n\tnumber.of.permutations = 10000,\n\ttest.aberrations       = '||ABERRATIONTYPE||')","source('||PLUGINSCRIPTDIRECTORY||aCGH/acgh-plot-survival.R')","acgh.plot.survival(\n\tsurvival             = 'Overall survival time',\n\tstatus               = 'Survival status',\n\taberrations          = '||ABERRATIONTYPE||',\n\tconfidence.intervals = '||CONFIDENCEINTERVALS||')"]},"renderer":{"GSP":"/aCGHSurvivalAnalysis/aCGHSurvivalAnalysisOutput"},"view":"aCGHSurvivalAnalysis"}