Question: MethylMix takes so much time for preprocess step
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gravatar for serbulentu
14 months ago by
serbulentu0
serbulentu0 wrote:

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   

 

 

methylmix • 179 views
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