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1
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1 args = commandArgs(trailingOnly=TRUE)
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2
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3 library("amap")
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4 library("labdsv")
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5
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6 data <- read.table("plink.raw")
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7 distances <- Dist(data[2:338,7:75189], method = "euclidean", nbproc = 144)
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4
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8 pco_results <- pco(distances,k=10)
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1
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9 #Variance explained by first three PCOs
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10 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0])
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11 #[1] 0.2565937
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12 pco_results$eig[2]/sum(pco_results$eig[pco_results$eig>0])
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13 #[1] 0.06878127
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14 pco_results$eig[3]/sum(pco_results$eig[pco_results$eig>0])
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15 #[1] 0.04340111
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16 write.csv(pco_results$points,file=args[1])
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17 write.csv(data[,2],file="PCO_sample_names.csv")
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