Upload process_genotype.R

process_genotype.R

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+library(snpStats)
+library(rrBLUP)
+library(sommer)
+
+args <- commandArgs(trailingOnly = TRUE)
+train_path <- args[1]
+test_path <- args[2]
+
+geno_Train <- read.csv(train_path, header = TRUE, stringsAsFactors = FALSE)
+geno_Test <- read.csv(test_path, header = TRUE, stringsAsFactors = FALSE)
+
+sample_ids_Train <- geno_Train[, 1]
+sample_ids_Test <- geno_Test[, 1]
+
+geno_Train <- as.matrix(geno_Train[, -1])
+geno_Test <- as.matrix(geno_Test[, -1])
+
+additive_Train <- A.mat(geno_Train)
+dominance_Train <- D.mat(geno_Train)
+additive_Test <- A.mat(geno_Test)
+dominance_Test <- D.mat(geno_Test)
+
+write.csv(data.frame(Sample_ID = sample_ids_Train, additive_Train), "Train_additive.csv", row.names = FALSE)
+write.csv(data.frame(Sample_ID = sample_ids_Train, dominance_Train), "Train_dominance.csv", row.names = FALSE)
+write.csv(data.frame(Sample_ID = sample_ids_Test, additive_Test), "Test_additive.csv", row.names = FALSE)
+write.csv(data.frame(Sample_ID = sample_ids_Test, dominance_Test), "Test_dominance.csv", row.names = FALSE)