calculate_resiliency: Internal Resiliency Function.

In abelew/stampr: Perform the STAMP analysis

Internal Resiliency Function.

Description

This is run for every experimental or calibration sample in the metadata.

Usage

calculate_resiliency(
  reference_vector,
  reads_df,
  cfu_vector,
  noiseless_table,
  sample_name,
  step_df,
  min_weight = 0.03,
  input_calibration = NULL,
  output_csv = "rtisan_values.csv",
  output_noiseless = "rtisan_noiseless.csv",
  innoculation_cfu = 1e+08,
  do_plots = FALSE,
  noise_correction = 0.005,
  verbose = FALSE
)

Arguments

reference_vector	Set of reference reads/tag.
reads_df	Table of the reads/tag for the samples of interest.
cfu_vector	Set of cfu values from which to acquire the target cfu for this particular sample.
noiseless_table	Input table of noisless data, currently unused.
sample_name	Name of this samples, used to extract some data.
step_df	Used to calculate the computed_bottleneck by stats::NLSstClosestX and generate the Ns value.
min_weight	Constant of the minimum weight!
input_calibration	Input calibration file, currently unused.
output_csv	Output csv file for writing new values.
innoculation_cfu	Assumed cfu when not provided.
do_plots	Print plots?
noise_correction	Constant for correcting noise!
verbose	Print text while running?

abelew/stampr documentation built on April 14, 2022, 5:03 a.m.