Mercurial > repos > cropgeeks > ukseed
diff dartseq_seeduk_2b.R @ 25:ae6b94d10bff draft
Uploaded
| author | cropgeeks |
|---|---|
| date | Fri, 20 Apr 2018 12:42:06 -0400 |
| parents | |
| children | d1d232d4cb2f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dartseq_seeduk_2b.R Fri Apr 20 12:42:06 2018 -0400 @@ -0,0 +1,17 @@ +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]) +