process_plate: Plate reader normalisation and calibration

In ucl-cssb/flopr: A package for the normalisation and calibration of flow cytometry and plate reader spectrophotometry data

Plate reader normalisation and calibration

Description

Plate reader normalisation and calibration

Usage

process_plate(
  data_csv,
  blank_well = "A1",
  neg_well = "A2",
  od_name = "OD",
  flu_names = c("GFP"),
  af_model = "spline",
  to_MEFL = F,
  flu_gains,
  conversion_factors_csv
)

Arguments

data_csv	path to a .csv file containing parsed plate reader data
blank_well	the well coordinates of one or more media blanks
neg_well	the well coordinates of a non-fluorescent control
od_name	the column name for the optical density data
flu_names	the column names for the fluorescence data
af_model	model used to fit negative control autofluorescence. For now these include "polynomial", "invers_poly", "exponential", "spline" and "loess".
to_MEFL	a Boolean to determine whether to attempt to convert OD and GFP reading to calibrated units
flu_gains	if to_MEFL=T, the gain values at which the fluorophores specified in flu_names was recorded. If there isn't calibration data for a fluorophore, do not speficy a gain value
conversion_factors_csv	if to_MEFL=T, path of the csv file containing conversion factors from plate reader calibration

Value

a data.frame with columns for raw plate reader data, normalised data and, if to_MEFL = T, calibrated OD and GFP data

ucl-cssb/flopr documentation built on Jan. 27, 2024, 11:49 a.m.