R/cal_scalefactor.R

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

#' @title cal_scalefactor
#'
#' @description used for generate a scale factor from bias-corrected Z score for TRS scale and normalization
#'
#' @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 most enriched cells will be selected to calculate scale factor
#'
#' @return a numeric value
#' @export
#'
#' @examples
#' \dontrun{ cal_scalefactor <- seedindx(z_score_mat$z_score, 0.01)}
#'
cal_scalefactor <- function(z_score, percent_cut=0.01){
  if(percent_cut<=0 | percent_cut>=1) {
    stop("percent_cut is a value between 0 and 1")
  }
  message("Scale factor is calculating from most enriched ", (100*percent_cut), "% of cells")
  sf_idx <- rank(-z_score) <= floor(percent_cut*length(z_score))
  sf <- mean(z_score[sf_idx])
  return(sf)
}