R/GAPIT.Burger.R

In jiabowang/GAPIT3: GAPIT (Genomic Association and Prediction Integrated Tool)

`GAPIT.Burger` <-
function(Y=NULL,CV=NULL,GK=NULL){
    #Object: To calculate likelihood, variances and ratio
    #Straitegy: NA
    #Output: P value
    #intput:
    #Y: phenotype with columns of taxa,Y1,Y2...
    #CV: covariate variables with columns of taxa,v1,v2...
    #GK: Genotype data in numerical format, taxa goes to row and snp go to columns. the first column is taxa (same as GAPIT.bread)
    #Authors: Xiaolei Liu ,Jiabo Wang and Zhiwu Zhang
    #Last update: November 2, 2015
##############################################################################################
    #print("GAPIT.Burger in progress...")
    
    if(!is.null(CV)){
        #CV=as.matrix(CV)#change CV to a matrix when it is a vector xiaolei changed here
		#theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV)) ###########for FarmCPU
		  theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])) #reseted by Jiabo ,CV frame is wrong,and not rm taxa
                                                         #############for GAPIT other method GWAS
    }else{
        theCV=matrix(1,nrow(Y),1)
    }
    
#handler of single column GK
n=nrow(GK)
m=ncol(GK)
if(m>2){
theGK=as.matrix(GK[,-1])
}else{
theGK=matrix(GK[,-1],n,1)
}

myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=theGK,X0=theCV   )
    REMLs=-2*myFaSTREML$LL
    delta=myFaSTREML$delta
    vg=myFaSTREML$vg
    ve=myFaSTREML$ve
    
    #print("GAPIT.Burger succeed!")
    return (list(REMLs=REMLs,vg=vg,ve=ve,delta=delta))
} #end of GAPIT.Burger.Bus
#=============================================================================================