R/pene.fn.logit.R

In zhanghfd/CCGA: Case-control genetic association analysis incorporating non-confounding covariates

pene.fn.logit <-
function(S,G,X,Y,par){
  if(length(par)-ncol(X)==2){
    if(ncol(X)==1){
      tmp = exp(par[1] + par[2]*G + as.numeric(X*par[-(1:2)]));
    }else{
      tmp = exp(par[1] + par[2]*G + as.numeric(X%*%par[-(1:2)]));
    }
  }else{
    if(ncol(X)==1){
      tmp = exp(par[1] + par[2]*S + par[3]*G + as.numeric(X*par[-(1:3)]));
    }else{
      tmp = exp(par[1] + par[2]*S + par[3]*G + as.numeric(X%*%par[-(1:3)]));
    }
  }
  return(1-Y+(2*Y-1)*tmp/(1+tmp));
}