## ----quick, echo=TRUE, message=FALSE, warning=FALSE, tidy=FALSE---------- library(DupChecker) ## Create a "DupChecker" directory under temporary directory rootDir<-paste0(dirname(tempdir()), "/DupChecker") dir.create(rootDir, showWarnings = FALSE) message(paste0("Downloading data to ", rootDir, " ...")) geoDownload(datasets=c("GSE1478"), targetDir=rootDir) arrayExpressDownload(datasets=c("E-MEXP-3872"), targetDir=rootDir) datafile<-buildFileTable(rootDir=rootDir, filePattern="cel$") result<-validateFile(datafile) if(result$hasdup){ duptable<-result$duptable write.csv(duptable, file=paste0(rootDir, "/duptable.csv")) } ## ----download, echo=TRUE, message=FALSE, warning=FALSE, tidy=FALSE------- datatable<-geoDownload(datasets = c("GSE1478"), targetDir=rootDir) datatable datatable<-arrayExpressDownload(datasets=c("E-MEXP-3872"), targetDir=rootDir) datatable ## ----buildFileTable, message=FALSE, warning=FALSE------------------------ datafile<-buildFileTable(rootDir=rootDir, filePattern="cel$") ## ----validateFile, message=FALSE, warning=FALSE-------------------------- result<-validateFile(datafile) if(result$hasdup){ duptable<-result$duptable write.csv(duptable, file=paste0(rootDir, "/duptable.csv")) } ## ----realexample, eval=FALSE, tidy=FALSE--------------------------------- # library(DupChecker) # # rootDir<-paste0(dirname(tempdir()), "/DupChecker_RealExample") # dir.create(rootDir, showWarnings = FALSE) # # geoDownload(datasets = c("GSE14333", "GSE13067", # "GSE17538"), targetDir=rootDir) # datafile<-buildFileTable(rootDir=rootDir, filePattern="cel$") # result<-validateFile(datafile) # if(result$hasdup){ # duptable<-result$duptable # write.csv(duptable, file=paste0(rootDir, "/duptable.csv")) # } ## ----sessInfo, echo=FALSE, results="asis"-------------------------------- toLatex(sessionInfo())