R/GAPIT.HapMap.R

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

`GAPIT.HapMap` <-
function(G,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator = FALSE, Major.allele.zero = FALSE){
    #Object: To convert character SNP genotpe to numerical
    #Output: Coresponding numerical value
    #Authors: Feng Tian and Zhiwu Zhang
    # Last update: May 30, 2011
    ##############################################################################################
    print(paste("Converting HapMap format to numerical under model of ", SNP.impute,sep=""))
    #gc()
    #GAPIT.Memory.Object(name.of.trait="HapMap.Start")
    
    #GT=data.frame(G[1,-(1:11)])
    if(heading){
        GT= t(G[1,-(1:11)])
        GI= G[-1,c(1,3,4)]
    }else{
        GT=NULL
        GI= G[,c(1,3,4)]
    }
    
    
    #Set column names
    if(heading)colnames(GT)="taxa"
    colnames(GI)=c("SNP","Chromosome","Position")
    
    #Initial GD
    GD=NULL
    bit=nchar(as.character(G[2,12])) #to determine number of bits of genotype
    #print(paste("Number of bits for genotype: ", bit))
    
    print("Perform numericalization")
    # Gtest=G[-1,-(1:11)]
    # print(Gtest[1:5,1:6])
    if(heading){
        if(!Create.indicator) GD= apply(G[-1,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
        if(Create.indicator) GD= t(G[-1,-(1:11)])
    }else{
        if(!Create.indicator) GD= apply(G[  ,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
        if(Create.indicator) GD= t(G[ ,-(1:11)])
    }
    
    #set GT and GI to NULL in case of null GD
    if(is.null(GD)){
        GT=NULL
        GI=NULL
    }
    # print(GD[1:6,1:5])
    
    
    if(!Create.indicator) {print(paste("Succesfuly finished converting HapMap which has bits of ", bit,sep="")) }
    return(list(GT=GT,GD=GD,GI=GI))
}#end of GAPIT.HapMap function
#=============================================================================================