R/runlinear.R

In IFAA: Robust Inference for Absolute Abundance in Microbiome Analysis

#-------------------------------------------------------------------
## function for cross validation using linear model
#-------------------------------------------------------------------

runlinear=function(
  x,
  y,
  nPredics,
  fwerRate=0.25,
  adjust_method="fdr"
){

  results=list()


  bootResu<-lm_sparse(x = x, y = y)
  
  p_value_est<-bootResu[,4]
  p_value_est_noint<-p_value_est[-seq(1,length(p_value_est),by=(nPredics+1))]
  p_value_est_noint_adj<-p.adjust(p_value_est_noint,adjust_method)
  p_value_est_noint_adj[is.na(p_value_est_noint_adj)]<-1

  coef_est<-abs(bootResu[,1])
  coef_est_noint<-coef_est[-seq(1,length(coef_est),by=(nPredics+1))]
  coef_est_noint[is.na(coef_est_noint)]<-max(coef_est_noint,na.rm = TRUE)


  # return
  results$betaNoInt=p_value_est_noint_adj<fwerRate
  results$betaInt=p_value_est
  results$coef_est_noint=coef_est_noint


  return(results)
}