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Collection of R scripts written for the data analysis and cleaning (mostly DNA methylation from TCGA)
Last updated July 22, 2012 These files have been written during my work at Sage Bionetworks and used for file processing and data analysis. List of scripts: BasicSVD.R BatchTraitsCorrelation.R BatchTraitsCorrelation_short.R chisqTest_testLevels.R combineGEOrawFiles.R combineTCGALevel3data.R createShortID.R factorConcat.R FtestPermut.R gunzipLoop.R Illumina450kTargetsDensity.R kMeansEvaluation.R MakesMethyLumiRobject_GBM.R MakesMethyLumiRobject.R mostVariableCpGsPerGene.R multipleMatch.R PCtechCorrelations.R README selectCpgWithMaxSD_perGene.R selectMostVarCpGs.R SurvivalBasicAnalysis.R TCGAcollectMethPvalue.R Each script is pretty well commented and explains what it does. Many of the scripts were created to deal with TCGA DNA methylation data, such as unpacking it, generating a single matrix from multiple Level1 files, creating short patient IDs from aliquot IDs, correlating batch with the clinical variables etc.
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