I try to use MethylMix on LUAD data. But it still waits after writing
Finding nonparametric adjustments
during 12 hours on a Xeon-E2620 server. The I use is below. Thanks for answers.
cancerSite <- "LUAD"
targetDirectory <- "/home/servertbb/Code/Bioinformatics/TCGA_DATA/MethylMix/"
cl <- makeCluster(10)
registerDoParallel(cl)
# Downloading methylation data
METdirectories <- Download_DNAmethylation(cancerSite, targetDirectory)
# Processing methylation data
METProcessedData <- Preprocess_DNAmethylation(cancerSite, METdirectories)
# Saving methylation processed data
saveRDS(METProcessedData, file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds"))
> sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=tr_TR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=tr_TR.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=tr_TR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.4.3 tools_3.4.3