Mercurial > repos > cropgeeks > ukseed
comparison dartseq_seeduk_2b.R @ 28:27777dd17bfe draft default tip
Uploaded
| author | cropgeeks |
|---|---|
| date | Sun, 22 Apr 2018 15:23:50 -0400 |
| parents | d1d232d4cb2f |
| children |
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| 27:558a46a635a9 | 28:27777dd17bfe |
|---|---|
| 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 rownames(data) <- data[,2] | |
| 7 distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = as.integer(args[2])) | 8 distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = as.integer(args[2])) |
| 8 pco_results <- pco(distances,k=10) | 9 pco_results <- pco(distances,k=10) |
| 9 #Variance explained by first three PCOs | 10 #Variance explained by first three PCOs |
| 10 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0]) | 11 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0]) |
| 11 #[1] 0.2565937 | 12 #[1] 0.2565937 |