R/seedindx.R

In fl-yu/SCAVENGE: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

#' @title seedindx
#'
#' @description used for generate seed cell index from bias-corrected Z score
#'
#' @param z_score a numeric vector that is original Z scores for individual cells calculated from gchromVAR
#' @param percent_cut a numeric number (0, 1) indicating what percentage of cells will be selected as seed cells if too many cells fit the P value<0.05 cutoff
#'
#' @return a logical vector indicating seed cells or not
#' @export
#'
#' @importFrom stats pnorm
#'
#' @examples
#' \dontrun{ seed_idx <- seedindx(z_score_mat$z_score, 0.1)}
#'
seedindex <- function(z_score, percent_cut=0.05){
  if(percent_cut<=0 | percent_cut>=1) {
    stop("percent_cut is a value between 0 and 1")
  }
  z2pvalue <- pnorm(z_score, lower.tail = FALSE)
  message("Cells with enriched P < 0.05: ", sum(z2pvalue<=0.05))
  s_percent <- round(sum(z2pvalue<=0.05)*100/length(z2pvalue), 2)
  message("Percent: ", s_percent, "%")
  if(s_percent>(100*percent_cut)){
    message("The top ", (100*percent_cut), "% of cells ", "(N=", floor(percent_cut*length(z2pvalue)), ") were selected as seed cells")
    seed_idx <- rank(-z_score) <= floor(percent_cut*length(z2pvalue))
  } else {
    message("These cells were selected as seed cells")
    seed_idx <- z2pvalue<=0.05
  }
  return(seed_idx)
}