R/SMUT.R

In wjzhong/SMUT: Multi-SNP Mediation Intersection-Union Test

SMUT=function(G,mediator,outcome,covariates=NULL,outcome_type="continuous",method="score",
              approxi=TRUE, debug=FALSE){

  # p_value_theta is the p value for testing theta in the outcome model
  # outcome model: outcome ~ intercept + G*gamma + mediator*theta + error
  p_value_theta=Testing_coefficient_of_mediator(G = G, mediator = mediator, outcome = outcome, covariates = covariates, 
                                                outcome_type = outcome_type, method = method, approxi = approxi, debug = debug)

  # p_value_beta is the p value for testing beta in the mediator model
  # mediator model: mediator ~ intercept + G*beta + error
  
  if (is.null(covariates)){
    obj=SKAT_Null_Model(mediator~1,out_type="C")
    p_value_beta=SKAT( as.matrix(G), obj,impute.method="bestguess")$p.value
  }else{
    obj=SKAT_Null_Model(mediator~covariates,out_type="C")
    p_value_beta=SKAT( as.matrix(G), obj,impute.method="bestguess")$p.value
  }
  

  # p_value_IUT is the p value for testing theta*beta based on intersection-union test
  p_value_IUT=max(c(p_value_theta,p_value_beta))
  return(list("p_value_IUT"=p_value_IUT,"p_value_theta"=p_value_theta,"p_value_beta"=p_value_beta))
}