Mercurial > repos > cropgeeks > ukseed
comparison dartseq_seeduk_2b.R @ 26:d1d232d4cb2f draft
Uploaded
| author | cropgeeks |
|---|---|
| date | Fri, 20 Apr 2018 14:44:25 -0400 |
| parents | ae6b94d10bff |
| children | 27777dd17bfe |
comparison
equal
deleted
inserted
replaced
| 25:ae6b94d10bff | 26:d1d232d4cb2f |
|---|---|
| 2 | 2 |
| 3 library("amap") | 3 library("amap") |
| 4 library("labdsv") | 4 library("labdsv") |
| 5 | 5 |
| 6 data <- read.table("plink.raw",header=T) | 6 data <- read.table("plink.raw",header=T) |
| 7 distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = 144) | 7 distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = as.integer(args[2])) |
| 8 pco_results <- pco(distances,k=10) | 8 pco_results <- pco(distances,k=10) |
| 9 #Variance explained by first three PCOs | 9 #Variance explained by first three PCOs |
| 10 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0]) | 10 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0]) |
| 11 #[1] 0.2565937 | 11 #[1] 0.2565937 |
| 12 pco_results$eig[2]/sum(pco_results$eig[pco_results$eig>0]) | 12 pco_results$eig[2]/sum(pco_results$eig[pco_results$eig>0]) |