R/GCN.R

In roqe/MACtest:

#' @import GBJ
#' @import CompQuadForm
#' @import ACAT
#' @export
GCN=function(S,M,Y,X,PS){
  gVCT=VCT(S,M,Y,X)
  if(is.na(PS$M_hat)){
    fit.m=lm(M~S+.,data = X)
    as=sign(sum(fit.m$coefficients["S",]))
    fit.y=glmnet::glmnet(cbind(M,S,X)[!is.na(Y),], Y[!is.na(Y)])
    bs=sign(sum(fit.y$beta[1:ncol(M),ncol(fit.y$beta)]))
    return(list(VCT=list(za=safe_z(gVCT$pa)*as,zb=safe_z(gVCT$pb)*bs),
                TSQ=list(za=NA,zb=NA),
                GBJ=list(za=NA,zb=NA),
                GHC=list(za=NA,zb=NA),
                mnP=list(za=NA,zb=NA),
                ACAT=list(za=NA,zb=NA)))
  }
  MA=round(cov2cor(PS$M_hat$covA),digits = 4)
  MB=round(cov2cor(PS$M_hat$covB),digits = 4)
  aTSQ=TSQ(PS$M_hat$a,MA)$pv
  bTSQ=TSQ(PS$M_hat$b,MB)$pv
  aGBJ=GBJ::GBJ(PS$M_hat$a,MA)$GBJ_pvalue
  bGBJ=GBJ::GBJ(PS$M_hat$b,MB)$GBJ_pvalue
  # if(aGBJ==1) aGBJ=GBJ::BJ(PS$P_hat$a,round(cov2cor(PS$P_hat$covA),digits = 4))$BJ_pvalue
  # if(bGBJ==1) bGBJ=GBJ::BJ(PS$P_hat$b,round(cov2cor(PS$P_hat$covB),digits = 4))$BJ_pvalue
  aGHC=GBJ::GHC(PS$M_hat$a,MA)$GHC_pvalue
  bGHC=GBJ::GHC(PS$M_hat$b,MB)$GHC_pvalue
  amnP=GBJ::minP(PS$M_hat$a,MA)$minP_pvalue
  bmnP=GBJ::minP(PS$M_hat$b,MB)$minP_pvalue
  aCAT=ACAT::ACAT(2*pnorm(abs(PS$M_hat$a),lower.tail = F))
  bCAT=ACAT::ACAT(2*pnorm(abs(PS$M_hat$b),lower.tail = F))
  return(list(VCT=list(za=safe_z(gVCT$pa)*PS$signAB$as,zb=safe_z(gVCT$pb)*PS$signAB$bs),
              TSQ=list(za=safe_z(aTSQ)*PS$signAB$as,zb=safe_z(bTSQ)*PS$signAB$bs),
              GBJ=list(za=safe_z(aGBJ)*PS$signAB$as,zb=safe_z(bGBJ)*PS$signAB$bs),
              GHC=list(za=safe_z(aGHC)*PS$signAB$as,zb=safe_z(bGHC)*PS$signAB$bs),
              minP=list(za=safe_z(amnP)*PS$signAB$as,zb=safe_z(bmnP)*PS$signAB$bs),
              ACAT=list(za=safe_z(aCAT)*PS$signAB$as,zb=safe_z(bCAT)*PS$signAB$bs)))
}