JunhuiLi1017/JM4QTN
Joint Mapping for QTN

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R/FreGeno.R

R/FreGeno.R
In JunhuiLi1017/JM4QTN: Joint Mapping for QTN 

FreGeno <-
function(CrosType,Gn=2,i,x,y=0){
  if(Gn<=1){
    stop(" Gn should > 0")
  }
  if(y != 0){
    z <- x + y -2*x*y
    if(CrosType == "Fn"){
      mtGeFre <- matrix(data=c(0), nrow = 50, ncol = 20)	##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn and ncol is 1~20.
      mtGeFre[1,20] <- 1	 ##mtGeFre[1,20]=1 means the Frequency of F1 which comes frome AAQQBB * aaqqbb -> AaQqBb equals to 1.
      for (g in 2:Gn){
        #AQB/AQB or aqb/aqb
        mtGeFre[g,1] <- 0.25*(4*mtGeFre[g-1,1]+mtGeFre[g-1,5]+mtGeFre[g-1,6]+(1-y)*(1-y)*mtGeFre[g-1,7]+mtGeFre[g-1,8]+(1-z)*(1-z)*mtGeFre[g-1,9]+
                                (1-x)*(1-x)*mtGeFre[g-1,10]+y*y*mtGeFre[g-1,11]+z*z*mtGeFre[g-1,13]+x*x*mtGeFre[g-1,16]+ x*x*(1-y)*(1-y)*mtGeFre[g-1,17]+
                                x*x*y*y*mtGeFre[g-1,18]+y*y*(1-x)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,20])
        #AQb/AQb or aqB/aqB
        mtGeFre[g,2] <- 0.25*(4*mtGeFre[g-1,2]+mtGeFre[g-1,5]+y*y*mtGeFre[g-1,7]+z*z*mtGeFre[g-1,9]+(1-x)*(1-x)*mtGeFre[g-1,10]+(1-y)*(1-y)*mtGeFre[g-1,11]+
                                mtGeFre[g-1,12]+(1-z)*(1-z)*mtGeFre[g-1,13]+mtGeFre[g-1,14]+x*x*mtGeFre[g-1,16]+ x*x*y*y*mtGeFre[g-1,17]+
                                x*x*(1-y)*(1-y)*mtGeFre[g-1,18]+(1-y)*(1-y)*(1-x)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*y*y*mtGeFre[g-1,20])
        #AqB/AqB or aQb/aQb
        mtGeFre[g,3] <- 0.25*(4*mtGeFre[g-1,3]+mtGeFre[g-1,6]+y*y*mtGeFre[g-1,7]+(1-z)*(1-z)*mtGeFre[g-1,9]+x*x*mtGeFre[g-1,10]+
                                (1-y)*(1-y)*mtGeFre[g-1,11]+z*z*mtGeFre[g-1,13]+mtGeFre[g-1,14]+mtGeFre[g-1,15]+(1-x)*(1-x)*mtGeFre[g-1,16]+ (1-x)*(1-x)*y*y*mtGeFre[g-1,17]+
                                (1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,18]+(1-y)*(1-y)*x*x*mtGeFre[g-1,19]+x*x*y*y*mtGeFre[g-1,20])
        #aQB/aQB or Aqb/Aqb
        mtGeFre[g,4] <- 0.25*(4*mtGeFre[g-1,4]+(1-y)*(1-y)*mtGeFre[g-1,7]+mtGeFre[g-1,8]+z*z*mtGeFre[g-1,9]+x*x*mtGeFre[g-1,10]+
                                y*y*mtGeFre[g-1,11]+mtGeFre[g-1,12]+(1-z)*(1-z)*mtGeFre[g-1,13]+mtGeFre[g-1,15]+(1-x)*(1-x)*mtGeFre[g-1,16]+ (1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,17]+
                                (1-x)*(1-x)*y*y*mtGeFre[g-1,18]+y*y*x*x*mtGeFre[g-1,19]+x*x*(1-y)*(1-y)*mtGeFre[g-1,20])
        #aqB/aqb or AQB/AQb
        mtGeFre[g,5] <- 0.5*(mtGeFre[g-1,5]+y*(1-y)*mtGeFre[g-1,7]+z*(1-z)*mtGeFre[g-1,9]+y*(1-y)*mtGeFre[g-1,11]+z*(1-z)*mtGeFre[g-1,13]+
                               x*x*y*(1-y)*mtGeFre[g-1,17]+x*x*y*(1-y)*mtGeFre[g-1,18]+y*(1-y)*(1-x)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*y*(1-y)*mtGeFre[g-1,20])
        #aqb/aQb or AqB/AQB
        mtGeFre[g,6] <- 0.5*(mtGeFre[g-1,6]+y*(1-y)*mtGeFre[g-1,7]+x*(1-x)*mtGeFre[g-1,10]+y*(1-y)*mtGeFre[g-1,11]+x*(1-x)*mtGeFre[g-1,16]+
                               x*y*(1-x)*(1-y)*mtGeFre[g-1,17]+x*y*(1-x)*(1-y)*mtGeFre[g-1,18]+x*y*(1-x)*(1-y)*mtGeFre[g-1,19]+x*y*(1-x)*(1-y)*mtGeFre[g-1,20])
        #aQB/aqb or Aqb/AQB
        mtGeFre[g,7] <- 0.5*((1-y)*(1-y)*mtGeFre[g-1,7]+y*y*mtGeFre[g-1,11]+ x*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,17]+x*y*y*(1-x)*mtGeFre[g-1,18]+
                               x*y*y*(1-x)*mtGeFre[g-1,19]+x*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,20])
        #Aqb/aqb or aQB/AQB
        mtGeFre[g,8] <- 0.5*(mtGeFre[g-1,8]+z*(1-z)*mtGeFre[g-1,9]+x*(1-x)*mtGeFre[g-1,10]+z*(1-z)*mtGeFre[g-1,13]+x*(1-x)*mtGeFre[g-1,16]+
                               x*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,17]+x*y*y*(1-x)*mtGeFre[g-1,18]+x*y*y*(1-x)*mtGeFre[g-1,19]+x*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,20])
        #AqB/aqb or aQb/AQB
        mtGeFre[g,9] <- 0.5*((1-z)*(1-z)*mtGeFre[g-1,9]+z*z*mtGeFre[g-1,13]+ x*(1-x)*(1-y)*y*mtGeFre[g-1,17]+x*y*(1-y)*(1-x)*mtGeFre[g-1,18]+
                               x*y*(1-y)*(1-x)*mtGeFre[g-1,19]+x*(1-x)*(1-y)*y*mtGeFre[g-1,20])
        #AQb/aqb or aqB/AQB
        mtGeFre[g,10] <- 0.5*((1-x)*(1-x)*mtGeFre[g-1,10]+x*x*mtGeFre[g-1,16]+ x*x*(1-y)*y*mtGeFre[g-1,17]+x*y*(1-y)*x*mtGeFre[g-1,18]+
                                (1-x)*y*(1-y)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*(1-y)*y*mtGeFre[g-1,20])
        #aqB/aQb or AqB/AQb
        mtGeFre[g,11] <- 0.5*(y*y*mtGeFre[g-1,7]+(1-y)*(1-y)*mtGeFre[g-1,11]+x*(1-x)*y*y*mtGeFre[g-1,17]+x*(1-y)*(1-y)*(1-x)*mtGeFre[g-1,18]+
                                x*(1-y)*(1-y)*(1-x)*mtGeFre[g-1,19]+x*y*(1-x)*y*mtGeFre[g-1,20])
        #aqB/aQB or Aqb/AQb
        mtGeFre[g,12] <- 0.5*(y*(1-y)*mtGeFre[g-1,7]+x*(1-x)*mtGeFre[g-1,10]+y*(1-y)*mtGeFre[g-1,11]+mtGeFre[g-1,12]+x*(1-x)*mtGeFre[g-1,16]+
                                x*(1-x)*y*(1-y)*mtGeFre[g-1,17]+x*(1-x)*y*(1-y)*mtGeFre[g-1,18]+x*(1-x)*y*(1-y)*mtGeFre[g-1,19]+x*(1-x)*y*(1-y)*mtGeFre[g-1,20])
        #aqB/Aqb or aQB/AQb
        mtGeFre[g,13] <- 0.5*(z*z*mtGeFre[g-1,9]+(1-z)*(1-z)*mtGeFre[g-1,13]+ x*(1-x)*(1-y)*y*mtGeFre[g-1,17]+x*y*(1-y)*(1-x)*mtGeFre[g-1,18]+
                                x*y*(1-y)*(1-x)*mtGeFre[g-1,19]+x*(1-x)*(1-y)*y*mtGeFre[g-1,20])
        #aqB/AqB or aQb/AQb
        mtGeFre[g,14] <- 0.5*(z*(1-z)*mtGeFre[g-1,9]+x*(1-x)*mtGeFre[g-1,10]+z*(1-z)*mtGeFre[g-1,13]+mtGeFre[g-1,14]+x*(1-x)*mtGeFre[g-1,16]+
                                x*(1-x)*y*y*mtGeFre[g-1,17]+x*(1-y)*(1-y)*(1-x)*mtGeFre[g-1,18]+x*(1-y)*(1-y)*(1-x)*mtGeFre[g-1,19]+x*y*y*(1-x)*mtGeFre[g-1,20])
        #aQb/aQB or Aqb/AqB
        mtGeFre[g,15] <- 0.5*(y*(1-y)*mtGeFre[g-1,7]+z*(1-z)*mtGeFre[g-1,9]+y*(1-y)*mtGeFre[g-1,11]+z*(1-z)*mtGeFre[g-1,13]+mtGeFre[g-1,15]+
                                y*(1-x)*(1-x)*(1-y)*mtGeFre[g-1,17]+y*(1-x)*(1-x)*(1-y)*mtGeFre[g-1,18]+x*x*y*(1-y)*mtGeFre[g-1,19]+x*x*y*(1-y)*mtGeFre[g-1,20])
        #aQb/Aqb or aQB/AqB
        mtGeFre[g,16] <- 0.5*(x*x*mtGeFre[g-1,10]+(1-x)*(1-x)*mtGeFre[g-1,16]+ (1-x)*(1-x)*(1-y)*y*mtGeFre[g-1,17]+(1-x)*(1-x)*(1-y)*y*mtGeFre[g-1,18]+
                                x*x*y*(1-y)*mtGeFre[g-1,19]+x*x*(1-y)*y*mtGeFre[g-1,20])
        #aQB/Aqb 
        mtGeFre[g,17] <- 0.5*((1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,17]+(1-x)*(1-x)*y*y*mtGeFre[g-1,18]+y*y*x*x*mtGeFre[g-1,19]+x*x*(1-y)*(1-y)*mtGeFre[g-1,20])
        #aQb/AqB
        mtGeFre[g,18] <- 0.5*((1-x)*(1-x)*y*y*mtGeFre[g-1,17]+(1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,18]+(1-y)*(1-y)*x*x*mtGeFre[g-1,19]+x*x*y*y*mtGeFre[g-1,20])
        #aqB/AQb
        mtGeFre[g,19] <- 0.5*(x*x*y*y*mtGeFre[g-1,17]+x*x*(1-y)*(1-y)*mtGeFre[g-1,18]+(1-y)*(1-y)*(1-x)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*y*y*mtGeFre[g-1,20])
        #aqb/AQB
        mtGeFre[g,20] <- 0.5*(x*x*(1-y)*(1-y)*mtGeFre[g-1,17]+x*x*y*y*mtGeFre[g-1,18]+y*y*(1-x)*(1-x)*mtGeFre[g-1,19]+(1-x)*(1-x)*(1-y)*(1-y)*mtGeFre[g-1,20])
      }
      rval <- mtGeFre[Gn,i]
    }else if(CrosType == "BCP1"){
      mtGeFre <- matrix(0,nrow=100,ncol=8)	 ##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn() and ncol is 1~8().
      mtGeFre[1,1] <- 1											##mtGeFre[1,1]=1 means the Frequency of F1 which comes frome AAQQBB * aaqqbb -> AaQqBb equals to 1.
      for (g in 2:Gn){
        # AQB/aqb
        mtGeFre[g,1] <- 0.5*(1-x)*(1-y)*mtGeFre[g-1,1]
        # AQB/aqB
        mtGeFre[g,2] <- 0.5*((1-x)*y*mtGeFre[g-1,1]+(1-x)*mtGeFre[g-1,2])
        # AQB/aQb
        mtGeFre[g,3] <- 0.5*(x*y*mtGeFre[g-1,1]+(1-z)*mtGeFre[g-1,3])
        # AQB/aQB
        mtGeFre[g,4] <- 0.5*(x*(1-y)*mtGeFre[g-1,1]+x*mtGeFre[g-1,2]+z*mtGeFre[g-1,3]+mtGeFre[g-1,4])
        # AQB/Aqb
        mtGeFre[g,5] <- 0.5*(x*(1-y)*mtGeFre[g-1,1]+(1-y)*mtGeFre[g-1,5])
        # AQB/AqB
        mtGeFre[g,6] <- 0.5*(x*y*mtGeFre[g-1,1]+x*mtGeFre[g-1,2]+y*mtGeFre[g-1,5]+mtGeFre[g-1,6])
        # AQB/AQb
        mtGeFre[g,7] <- 0.5*((1-x)*y*mtGeFre[g-1,1]+z*mtGeFre[g-1,3]+y*mtGeFre[g-1,5]+mtGeFre[g-1,7])
        # AQB/AQB
        mtGeFre[g,8] <- 0.5*((1-x)*(1-y)*mtGeFre[g-1,1]+(1-x)*mtGeFre[g-1,2]+(1-z)*mtGeFre[g-1,3]+mtGeFre[g-1,4]+(1-y)*mtGeFre[g-1,5]+mtGeFre[g-1,6]+mtGeFre[g-1,7])+mtGeFre[g-1,8]
      }
      rval <- mtGeFre[Gn,i]
    }else if(CrosType == "BCP2"){
      mtGeFre <- matrix(0,nrow=100,ncol=8)					##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn() and ncol is 1~8().
      mtGeFre[1,8] <- 1											##mtGeFre[1,1]=1 means the Frequency of F1 which comes frome AAQQBB * aaqqbb -> AaQqBb equals to 1.
      for (g in 2:Gn){
        # aqb/aqb
        mtGeFre[g,1] <- 0.5*((1-x)*(1-y)*mtGeFre[g-1,8]+(1-x)*mtGeFre[g-1,7]+(1-z)*mtGeFre[g-1,6]+mtGeFre[g-1,5]+(1-y)*mtGeFre[g-1,4]+mtGeFre[g-1,3]+mtGeFre[g-1,2])+mtGeFre[g-1,1]
        # aqb/aqB
        mtGeFre[g,2] <- 0.5*((1-x)*y*mtGeFre[g-1,8]+z*mtGeFre[g-1,6]+y*mtGeFre[g-1,4]+mtGeFre[g-1,2])
        # aqb/aQb
        mtGeFre[g,3] <- 0.5*(x*y*mtGeFre[g-1,8]+x*mtGeFre[g-1,7]+y*mtGeFre[g-1,4]+mtGeFre[g-1,3])
        # aqb/aQB
        mtGeFre[g,4] <- 0.5*(x*(1-y)*mtGeFre[g-1,8]+(1-y)*mtGeFre[g-1,4])
        # aqb/Aqb
        mtGeFre[g,5] <- 0.5*(x*(1-y)*mtGeFre[g-1,8]+x*mtGeFre[g-1,7]+z*mtGeFre[g-1,6]+mtGeFre[g-1,5])
        # aqb/AqB
        mtGeFre[g,6] <- 0.5*(x*y*mtGeFre[g-1,8]+(1-z)*mtGeFre[g-1,6])
        # aqb/AQb
        mtGeFre[g,7] <- 0.5*((1-x)*y*mtGeFre[g-1,8]+(1-x)*mtGeFre[g-1,7])
        # aqb/AQB
        mtGeFre[g,8] <- 0.5*(1-x)*(1-y)*mtGeFre[g-1,8]
      }
      rval <- mtGeFre[Gn,i]
    }else{
      stop("argument CrosType must be 'Fn' or 'BCP1' or 'BCP2'")
    }
  }else{
    if(CrosType == "Fn"){
      mtGeFre <- matrix(0,nrow=100,ncol=9)	 ##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn() and ncol is 1~4().
      mtGeFre[1,5] <- 1											##mtGeFre[1,1]=1 means the Frequency of F1 which comes frome AABB * aabb -> AaBb equals to 1.
      for (g in 2:Gn){
        # ab/ab
        mtGeFre[g,1] <- 0.25*(4*mtGeFre[g-1,1]+mtGeFre[g-1,2]+mtGeFre[g-1,4]+(1-x)^2*mtGeFre[g-1,5])
        # aB/ab
        mtGeFre[g,2] <- 0.25*(2*mtGeFre[g-1,2]+x*(1-x)*mtGeFre[g-1,5])
        # aB/aB
        mtGeFre[g,3] <- 0.25*(2*mtGeFre[g-1,2]+4*mtGeFre[g-1,3]+x^2*mtGeFre[g-1,5]+mtGeFre[g-1,6])
        # Ab/ab
        mtGeFre[g,4] <- 0.25*(2*mtGeFre[g-1,4]+x*(1-x)*mtGeFre[g-1,5])
        # AB/ab or Ab/aB
        mtGeFre[g,5] <- 0.25*((1-x)^2+x^2)*mtGeFre[g-1,5]
        # AB/aB
        mtGeFre[g,6] <- 0.25*(2*mtGeFre[g-1,6]+x*(1-x)*mtGeFre[g-1,5])
        # Ab/Ab
        mtGeFre[g,7] <- 0.25*(2*mtGeFre[g-1,8]+4*mtGeFre[g-1,7]+x^2*mtGeFre[g-1,5]+mtGeFre[g-1,4])
        # AB/Ab
        mtGeFre[g,8] <- 0.25*(2*mtGeFre[g-1,28]+x*(1-x)*mtGeFre[g-1,5])
        # ab/ab
        mtGeFre[g,9] <- 0.25*(4*mtGeFre[g-1,9]+mtGeFre[g-1,8]+mtGeFre[g-1,6]+(1-x)^2*mtGeFre[g-1,5])
        rval <- mtGeFre[Gn,i]
      }
    }else if(CrosType == "BCP1"){
      mtGeFre <- matrix(0,nrow=100,ncol=4)	 ##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn() and ncol is 1~4().
      mtGeFre[1,1] <- 1											##mtGeFre[1,1]=1 means the Frequency of F1 which comes frome AABB * aabb -> AaBb equals to 1.
      for (g in 2:Gn){
        # AB/ab
        mtGeFre[g,1] <- 0.5*(1-x)*mtGeFre[g-1,1]
        # AB/aB
        mtGeFre[g,2] <- 0.5*(x*mtGeFre[g-1,1]+mtGeFre[g-1,2])
        # AB/Ab
        mtGeFre[g,3] <- 0.5*(x*mtGeFre[g-1,1]+mtGeFre[g-1,3])
        # AB/AB
        mtGeFre[g,4] <- 0.5*((1-x)*mtGeFre[g-1,1]+mtGeFre[g-1,2]+mtGeFre[g-1,3])+mtGeFre[g-1,4]
      }
      rval <- mtGeFre[Gn,i]
    }else if(CrosType == "BCP2"){
      mtGeFre <- matrix(0,nrow=100,ncol=4)	 ##mtGeFre: Matrix of Frequency of the Genotypes ,where nrow is Gn() and ncol is 1~4().
      mtGeFre[1,4] <- 1											##mtGeFre[1,1]=1 means the Frequency of F1 which comes frome AABB * aabb -> AaBb equals to 1.
      for (g in 2:Gn){
        # ab/ab
        mtGeFre[g,1] <- 0.5*(mtGeFre[g-1,2]+mtGeFre[g-1,3]+(1-x)*mtGeFre[g-1,4])+mtGeFre[g-1,1]
        # ab/aB
        mtGeFre[g,2] <- 0.5*(mtGeFre[g,2]+x*mtGeFre[g-1,4])
        # ab/Ab
        mtGeFre[g,3] <- 0.5*(mtGeFre[g,3]+x*mtGeFre[g-1,4])
        # AB/AB
        mtGeFre[g,4] <- 0.5*(1-x)*mtGeFre[g-1,4]
      }
      rval <- mtGeFre[Gn,i]
    }else{
      stop("argument CrosType must be 'Fn' or 'BCP1' or 'BCP2'")
    }
  }
  return(rval)
}
JunhuiLi1017/JM4QTN documentation built on June 4, 2019, 4:10 a.m.

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