R/DACT.R

In zhonghualiu/DACT: Testing for mediation effects in genome-wide epigenetic studies.

#' DACT is a function used for testing for mediation effect in genome-wide epigenetic studies.
#' @param p_a, the p-value vector for the exposure-mediator associations
#' @param p_b, the p-value vector for the mediator-outcome associations
#' @param correction, the name of method for correction, either "Efron" or "JC". By default, it is set to NULL.
#' @return the p-value vector of mediation effect testing
#' @references Liu, Z. , Shen, J., Barfield, R., Schwartz, J., Baccarelli, A., Lin, X., 2020. Large-scale hypothesis testing for causal mediation effects in Genome-wide epigenetic studies. (under review)
#' @author Zhonghua Liu < zl2509@cumc.columbia.edu >
#' @usage DACT(p_a,p_b,correction)
#' @export
DACT = function(p_a,p_b,correction=NULL){
  Z_a = stats::qnorm(p_a,lower.tail = F)
  Z_b = stats::qnorm(p_b,lower.tail = F)
  pi0a = 1 - nonnullPropEst(Z_a,0,1)
  pi0b = 1 - nonnullPropEst(Z_b,0,1)
  #pi0a = locfdr::locfdr(Z_a,nulltype = 0)$fp0[5,3]
  #pi0b = locfdr::locfdr(Z_b,nulltype = 0)$fp0[5,3]
  if(pi0a > 1){
    pi0a = 1
  }
  if(pi0b >1){
    pi0b = 1
  }
  p.mat = cbind(p_a,p_b)
  p3 = (apply(p.mat,1,max))^2
  wg1 = pi0a*(1-pi0b)
  wg2 = (1-pi0a)*pi0b
  wg3 = pi0a*pi0b
  wg.sum = wg1 + wg2 + wg3
  wg.std = c(wg1,wg2,wg3)/wg.sum
  p_dact = wg.std[1]*p_a + wg.std[2]*p_b + wg.std[3]*p3
  if(correction == "Efron"){
  p_dact = EfronCorrect(p_dact)
  }
  if(correction == "JC"){
    p_dact = JCCorrect(p_dact)
  }
  return(p_dact)
}