rtisan_nr_nb: This is the top-level function from the authors. I have it...
In abelew/stampr: Perform the STAMP analysis

rtisan_nr_nb

R Documentation

This is the top-level function from the authors. I have it wrapped.

Description

It sets up the data and iterates over every experimental sample in order to run the calculate resliency function upon it.

Usage

rtisan_nr_nb(
  read_csv,
  cfu_vector,
  innoculation_cfu = 1e+08,
  chosen_seed = 1,
  reference_samples = c(1, 2, 3),
  min_weight = 0.03,
  noise_correction = 0.005,
  input_calibration = NULL,
  do_plots = FALSE,
  verbose = FALSE,
  output_csv = "rtisan_values.csv",
  output_noiseless = "rtisan_noiseless.csv",
  cpus = NULL,
  parallel = TRUE
)

Arguments

`read_csv`	CSV file containing the reads/tag, FIXME: use the tag data structure here to simplify things.
`cfu_vector`	CFU values for each sample of interest.
`innoculation_cfu`	Assumed cfu if they are not provided.
`chosen_seed`	Set the seed you maniacs!
`reference_samples`	Vector of reference samples, provided by the metadata via the parent function.
`min_weight`	Constant of minimum weight...
`noise_correction`	Constant of noise correction...
`input_calibration`	CSV of input calibrations.
`do_plots`	Plot the results?
`verbose`	Be verbose?
`output_csv`	Print the new Nb values here.
`output_noiseless`	Print the noiseless data here...