updatePhenotypes

# change/update phenotypes in PLINK files
# See the video tutorial on the Genomics Boot Camp YouTube channel

# Clear workspace
rm(list = ls())
# Set working directory
setwd("XXXXXXXXXXXXXXXXXXXXXXXXXX")

# update phenotype column - single phenotype in file
system("plink --file testData --pheno heightData.txt --recode --out phenoUpdated")

# update phenotype column - select a specific one from a list
system("plink --file testData --pheno PhenotypeMeasures.txt --mpheno 2 --recode --out phenoUpdated_weight_v1")

system("plink --file testData --pheno PhenotypeMeasures.txt --pheno-name weight --recode --out phenoUpdated_weight_v2")


# separate PLINK files for all phenotypes
# ATTENTION!!! Might take a lot of HDD space - ped+map file for each phenotype

nrMeasures <- 3 # this is how many phenotype measurements you have in the PhenotypeMeasures.txt file
for (i in 1:nrMeasures) {
  system(
    paste0("plink --file testData --pheno PhenotypeMeasures.txt --mpheno ", i,
           " --recode --out phenoUpdated_trait",i))
}


# separate PLINK files for all phenotypes - named pheotypes
# ATTENTION!!! Might take a lot of HDD space - ped+map file for each phenotype
nrMeasures <- c("height", "weight", "shoeSize") # this is how many phenotype measurements you have in the PhenotypeMeasures.txt file

for (i in 1:length(nrMeasures)) {
  system(
    paste0("plink --file testData --pheno PhenotypeMeasures.txt --pheno-name ", nrMeasures[i],
           " --recode --out phenoUpdated_trait_",nrMeasures[i]))

  #GWAS

  #visualization

}