R/VarInt.cc.pD.R

In clinUtiDNA: Clinical Utility of DNA Testing

VarInt.cc.pD <- 
function(pD,XY){
X1=XY[1];  X2=XY[2]; X3=XY[3]; X4=XY[4];
Y1=XY[5];  Y2=XY[6]; Y3=XY[7]; Y4=XY[8];

n1 <- X1+X2+X3+X4; n0 <- Y1+Y2+Y3+Y4
q <- pD*n0/(1-pD)/n1
res <- q^2*((X2^2*(n0 - Y2)*Y2)/(n0*(q*X2 + Y2)^4) + X1^2*(-(((n0 + n1)*Y1^2)/(n0*n1*(q*X1 + Y1)^4)) - Y2^2/(n1*(q*X2 + Y2)^4) +
    Y1*((q*X1 + Y1)^(-4) + (2*Y2)/(n1*(q*X1 + Y1)^2*(q*X2 + Y2)^2))) + (X3^2*Y3)/(q*X3 + Y3)^4 + (X3*Y3^2)/(q*X3 + Y3)^4 - (X3^2*Y3^2)/(n0*(q*X3 + Y3)^4) -
  (X3^2*Y3^2)/(n1*(q*X3 + Y3)^4) + (X4^2*Y4)/(q*X4 + Y4)^4 + (X4*Y4^2)/(q*X4 + Y4)^4 - (X4^2*Y4^2)/(n0*(q*X4 + Y4)^4) - (X4^2*Y4^2)/(n1*(q*X4 + Y4)^4) +
  (2*X3*X4*Y3*Y4)/(n0*(q*X3 + Y3)^2*(q*X4 + Y4)^2) + (2*X3*X4*Y3*Y4)/(n1*(q*X3 + Y3)^2*(q*X4 + Y4)^2) +
  (2*X2*Y2*(-(X4*Y3) + X3*Y4)*(q^2*X3*X4 - Y3*Y4))/(n0*(q*X2 + Y2)^2*(q*X3 + Y3)^2*(q*X4 + Y4)^2) +
  X1*(Y1^2/(q*X1 + Y1)^4 + (Y2*(Y2 - (2*X3*(q*X2 + Y2)^2*Y3)/(n1*(q*X3 + Y3)^2) + (2*X4*(q*X2 + Y2)^2*Y4)/(n1*(q*X4 + Y4)^2)))/(q*X2 + Y2)^4 +
    (2*Y1*(((X3*Y3)/(q*X3 + Y3)^2 - (X4*Y4)/(q*X4 + Y4)^2)/n1 + ((X2*Y2)/(q*X2 + Y2)^2 + (X3*Y3)/(q*X3 + Y3)^2 - (X4*Y4)/(q*X4 + Y4)^2)/n0))/(q*X1 + Y1)^2))

return(res)
}