options(warn=-1) #library(affxparser) #library(affy) library(R.utils) #library(Matrix) ##library(multtest) #library(limma) #library(Amelia) #library(Zelig) #library(impute) #library(pcaMethods) #library(mice) #scratch <- Sys.getenv("UABGRID_SCRATCH") #scratch <- paste(scratch,"/maqc",sep="") #setwd(scratch) #for (MissingMethod in c("mcar", "mar", "nmar")) { #for (MissingMethod in c("mar")) { # results <- NULL # for (task.id in 1:1000) { # for (miss.idx in c(1, 2, 3, 4)) { # fname <- paste("ImputationResults",MissingMethod,miss.idx,"_",task.id,".csv",sep="") # if (file.exists(fname)) { # one.result <- read.table(fname,sep=",",header=TRUE) # results <- rbind(results,one.result) # } else { # writeLines("Missing data") # print(fname) # print(miss.idx) # print(task.id) # print(MissingMethod) # } # } # } # write.table(results,file=paste("ImputationMAQCResults",MissingMethod,"092210.csv",sep=""),sep=",",row.names=FALSE,col.names=TRUE) #} for (MissingMethod in c("mcar")) { results <- NULL #task.id <- 1001 for (task.id in 1:12000) { task.num <- as.integer(task.id)-1 task.string <- toString(task.num) task.string <- paste("0000",task.string,sep="") task.string <- substr(task.string,nchar(task.string)-3,nchar(task.string)) thousands <- substr(task.string,1,1) hundreds <- substr(task.string,2,2) tens <- substr(task.string,3,3) ones <- substr(task.string,4,4) set.seed(task.num+1) sim.idx <- (task.num %% 1000) + 1 missimp <- floor(task.num/1000)+1 #miss.idx <- floor(missimp/4)+1 #imp.idx <- (missimp %% 4)+1 miss.pct <- rep(c(0.05, 0.10, 0.20, 0.30), each=3) imp.num <- rep(c(5,10,20),times=4) targetp <- miss.pct[missimp] num.impute <- imp.num[missimp] user <- Sys.getenv("USER") scratch <- Sys.getenv("UABGRID_SCRATCH") .libPaths(c("/home/rekenned/R/x86_64-unknown-linux-gnu-library/2.8", "/share/apps/R/R-2.8.1/gnu/lib/R/bioc", "/share/apps/R/R-2.8.1/gnu/lib/R/library")) celdir <- paste(scratch,"/ImputationSim/",sep="") destdir <- paste(scratch,"/ImputationSim/",thousands,"/",hundreds,"/",tens,"/",ones,"/",sep="") job.name <- Sys.getenv("JOB_NAME") job.id <- Sys.getenv("JOB_ID") setwd(destdir) fname <- paste("ImputationSim",num.impute,"Results",MissingMethod,miss.pct*100,"_",sim.idx,".csv",sep="") if (file.exists(fname)) { print(fname) one.result <- read.table(fname,sep=",",header=TRUE) results <- rbind(results,one.result) } else { writeLines("Missing data") print(fname) print(miss.idx) print(task.id) print(MissingMethod) } } setwd(celdir) write.table(results,file=paste("ImputationSim",num.impute,"Results",MissingMethod,targetp*100,"_042911.csv",sep=""),sep=",",row.names=FALSE,col.names=TRUE) } #table.data <- #data.frame(miss.pct=miss.pct[miss.idx],simulation=sim.idx,lrmse.bpca=lrmse.bpca,lrmse.knn=lrmse.knn,lrmse.lls=lrmse.lls,lrmse.amelia=lrmse.amelia,lrmse.mice=lrmse.mice,diff.total=found.total,diff.orig=found.orig,diff.bpca=found.bpca,diff.knn=found.knn,diff.lls=found.lls,found.amelia1,found.amelia2,found.amelia3,found.amelia4,found.amelia5,found.amelia6,found.amelia7,found.amelia8,found.amelia9,found.mice1,found.mice2,found.mice3,found.mice4,found.mice5,found.mice6,found.mice7,found.mice8,found.mice9) #write.table(table.data,file=paste("ImputationResults",MissingMethod,miss.idx,"_",sim.idx,".csv",sep=""),sep=",",row.names=FALSE,col.names=TRUE) #print(table.data)