source("http://zzlab.net/GAPIT/gapit_functions.txt") #Import demo data myGD=read.table(file="http://zzlab.net/GAPIT/data/mdp_numeric.txt",head=T) myGM=read.table(file="http://zzlab.net/GAPIT/data/mdp_SNP_information.txt",head=T) #Simultate 10 QTN on the first half chromosomes index1to5=myGM[,2]<6 set.seed(99164) mySim=GAPIT.Phenotype.Simulation(GD=myGD[,c(TRUE,index1to5)],GM=myGM[index1to5,],h2=.7,NQTN=40, effectunit =.95,QTNDist="normal") #GWAS with GAPIT myGAPIT=GAPIT(Y=mySim$Y,GD=myGD,GM=myGM,PCA.total=3, QTN.position=mySim$QTN.position, model=c("GLM", "MLM", "CMLM", "SUPER", "MLMM", "FarmCPU", "Blink"))