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#!/usr/bin/env Rscript
# @(#)GWAS_boxcox 2016-09-07 A.Douglas and A.J.Travis
if (!require("forecast")) install.packages("forecast")
# command-line arguments from argv
args <- commandArgs(trailingOnly = TRUE)
# input file
input <- args[1]
# output file
output <- args[2]
box_cox_df <- function(x) {
trans_pheno <- matrix(NA, nrow = nrow(x), ncol = (ncol(x) - 2))
colnames(trans_pheno) <- colnames(x)[-c(1:2)]
lambda <- rep(NA, ncol(trans_pheno))
accs <- x[,1:2]
for(i in 3:ncol(x)){
lambda[i - 2] = BoxCox.lambda(x[,i])
trans_pheno[,i - 2] = BoxCox(x[,i], lambda[i - 2])
}
trans_pheno <- cbind(accs, as.data.frame(trans_pheno))
return(list(trans = trans_pheno, lambda = lambda))
}
# read phenotype file
data <- read.table(file = input, header = FALSE)
result <- box_cox_df(data)
data <- result$trans
lambda <- result$lambda
print(lambda)
write.table(data, file = output, row.names = FALSE, col.names = FALSE, quote = FALSE)
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