R/runlinear.R

In quranwu/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)
}