Noise removal function — rm_noise • denoisingCTF

This function removes the beads and debris from FCS files using trained classification models. It writes new FCS files with denoised data and also writes CSV files of the original data with the added columns of beads and debris that contains the classification information in case the user wants to explore the results.

rm_noise(
  file_type = ".fcs|.FCS",
  rm_beads = TRUE,
  rm_debris = TRUE,
  use.current.model.beads = TRUE,
  use.current.model.debris = TRUE,
  model_beads = model_beads,
  model_debris = model_debris,
  alg_db = "RF",
  alg_bd = "RF"
)

Arguments

file_type	A regular expression for the file extension. Only file names which match the regular expression will be returned. FCS only.
rm_beads	Logical. If `TRUE` beads are removed. Default is `TRUE`.
rm_debris	Logical. If `TRUE` debris is removed. Default is `TRUE`.
use.current.model.beads	Logical. If `FALSE`, an object of class `train` can be passed to the argument `model_beads`. Default is `TRUE`.
use.current.model.debris	Logical. If `FALSE`, an object of class `train` can be passed to the argument `model_beads`. Default is `TRUE`.
model_beads	Object of class `train`. Needed if `use.current.model.beads` is `FALSE`.
model_debris	Object of class `train`. Needed if `use.current.model.debris` is `FALSE`.
alg_db	A character vector with the name of the algorithm used to train `model_beads`. It can be 'RF' for Random Forest or 'XGB' for XGBoost.
alg_bd	A character vector with the name of the algorithm used to train `model_beads`. It can be 'RF' for Random Forest or 'XGB' for XGBoost.