{"id":"pca","name":"PCA","dataTypes":{"subset1":["CLINICAL.TXT"]},"dataFileInputMapping":{"CLINICAL.TXT":"FALSE","SNP.TXT":"snpData","MRNA_DETAILED.TXT":"TRUE"},"pivotData":false,"variableMapping":{"||GENES||":"divIndependentVariablePathway","||AGGREGATE||":"divIndependentVariableprobesAggregation","||GPL1||":"divIndependentVariablegplsValue","||GPL2||":"divIndependentVariablegplsValue2","||SAMPLE1||":"divIndependentVariablesamples","||SAMPLE2||":"divIndependentVariablesamples2","||TIMEPOINTS1||":"divIndependentVariabletimepoints","||TIMEPOINTS2||":"divIndependentVariabletimepoints2","||TISSUES1||":"divIndependentVariabletissues","||TISSUES2||":"divIndependentVariabletissues2"},"converter":{"R":["source('||PLUGINSCRIPTDIRECTORY||Common/dataBuilders.R')","source('||PLUGINSCRIPTDIRECTORY||Common/ExtractConcepts.R')","source('||PLUGINSCRIPTDIRECTORY||Common/collapsingData.R')","source('||PLUGINSCRIPTDIRECTORY||Common/parseDirectory.R')","source('||PLUGINSCRIPTDIRECTORY||PCA/BuildPCAData.R')","parseDirectory(topLevelDirectory = '||TOPLEVELDIRECTORY||')","PCAData.build(\n        input.gexFile    = '||TOPLEVELDIRECTORY||/workingDirectory/mRNA.trans',\n        sample.subset1   = '||SAMPLE1||',\n        time.subset1     = '||TIMEPOINTS1||',\n        tissues.subset1  = '||TISSUES1||',\n        platform.subset1 = '||GPL1||',\n        sample.subset2   = '||SAMPLE2||',\n        time.subset2     = '||TIMEPOINTS2||',\n        tissues.subset2  = '||TISSUES2||',\n        platform.subset2 = '||GPL2||',\n        genes            = '||GENES||',\n        genes.aggregate  = '||AGGREGATE||')"]},"processor":{"R":["source('||PLUGINSCRIPTDIRECTORY||PCA/LoadPCA.R')","PCA.loader(input.filename='outputfile')"]},"renderer":{"GSP":"/PCA/pcaOut"},"view":"PCA"}