diff dartseq_seeduk_2.R @ 1:a8f30e5859c9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dartseq_seeduk_2.R	Tue Apr 17 08:09:21 2018 -0400
@@ -0,0 +1,17 @@
+args = commandArgs(trailingOnly=TRUE)
+
+library("amap")
+library("labdsv")
+
+data <- read.table("plink.raw")
+distances <- Dist(data[2:338,7:75189], method = "euclidean", nbproc = 144)
+pco_results <- cmdscale(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])
+write.csv(data[,2],file="PCO_sample_names.csv")