install.packages("bigmemory")
install.packages("biganalytics")
install.packages("foreach")
install.packages("biglm")
install.packages("DBI")
library("bigmemory")

library("foreach")
library("biglm")
library("DBI")
library("biganalytics")
library("compiler") #this library is already installed in R
install.packages ("ape")
install.packages ("EMMREML")
install.packages ("Matrix")
install.packages ("scatterplot3d")
library("ape")
library("EMMREML")
library("Matrix")
library("scatterplot3d")
source("http://zzlab.net/GAPIT/gapit_functions.txt")
source("http://zzlab.net/FarmCPU/FarmCPU_functions.txt")
library("bigmemory")
library("biganalytics")
library("compiler") #this library is already installed in R
source("http://zzlab.net/GAPIT/gapit_functions.txt")
source("http://zzlab.net/FarmCPU/FarmCPU_functions.txt")
setwd("C:\\myFarmCPU") #example for windows; if you use linux or mac, change the file path in the quote
#Step 1: Set working directory and import data
setwd("C:\\myFarmCPU")
myY <-read.table("mdp_traits.txt", head = TRUE)
myG <-read.table("mdp_genotype.txt", head = FALSE)
myGAPIT <-GAPIT(G=myG, output.numerical=TRUE)
install.packages ("LDheatmap")
library("LDheatmap")
myGD= myGAPIT$GD
myGM= myGAPIT$GM


FarmCPU.P.Threshold(
  Y=myY[,c(1,3)],
  GD=myGD,
  GM=myGM, 
  trait="StoverYield",
  theRep=1000)


myFarmCPU<-FarmCPU(
  Y=myY[,c(1,4)],
  GD=myGD,
  GM=myGM, 
  p.threshold=2.59E-06, #para un genome-wise error of 0.10
  maxLoop=10,
  method.bin="optimum",
  bin.size=c(5e5,5e6,5e7), #default set of bin.size
  bin.selection=seq(10,100,10) #default set of bin.select,
)