Mercurial > repos > cropgeeks > ukseed
view dartseq_seeduk_2b.R @ 25:ae6b94d10bff draft
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| author | cropgeeks |
|---|---|
| date | Fri, 20 Apr 2018 12:42:06 -0400 |
| parents | |
| children | d1d232d4cb2f |
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args = commandArgs(trailingOnly=TRUE) library("amap") library("labdsv") data <- read.table("plink.raw",header=T) distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = 144) pco_results <- pco(distances,k=10) #Variance explained by first three PCOs pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0]) #[1] 0.2565937 pco_results$eig[2]/sum(pco_results$eig[pco_results$eig>0]) #[1] 0.06878127 pco_results$eig[3]/sum(pco_results$eig[pco_results$eig>0]) #[1] 0.04340111 write.csv(pco_results$points,file=args[1])