R code for Genome Wide Association studies

if (!requireNamespace("BiocManager", quietly = TRUE)) 
  install.packages("BiocManager") 

BiocManager::install("http://bioconductor.org/biocLite.R") 
install.packages("BiocManager") 
BiocManager::install("multtest") 

library(BiocManager) 
library(multtest) 

install.packages("gplots") 
install.packages("genetics") 
install.packages("ape") 
install.packages("EMMREML") 
install.packages("scatterplot3d") 

library(multtest) 
library(gplots) 
library(genetics) 
library(ape) 
library(EMMREML) 
library(compiler) # this library is already installed in R 
library(scatterplot3d) 

source("http://zzlab.net/GAPIT/gapit_functions.txt") 
source("http://zzlab.net/GAPIT/emma.txt") 

myY <- read.table("mdp_traits.txt", head = TRUE) 
myG <- read.delim("mdp_genotype_test.hmp.txt", head = FALSE) 

# Step 2: Run GAPIT 
myGAPIT <- GAPIT(
  Y = myY,
  G = myG,
  PCA.total = 3,
  model = c("GLM", "MLM", "MLMM", "FarmCPU", "Blink")
)