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Calculate FP concentration in molar units

Source: R/calc_fpconc.R
calc_fpconc.Rd

Takes as input plate reader data processed with process_plate() and uses normalised/calibrated values to calculate FP concentration. Adds column(s) for FP concentration as either: (a) normalisedFP/cellvolume (RFU/L), (b) calibratedFP/cellvolume (moles/L, or M). Plots results and returns a dataframe.

Usage

calc_fpconc(
  data_csv,
  timecourse = TRUE,
  flu_channels,
  flu_labels,
  remove_wells,
  get_rfu_vol = TRUE,
  get_mol_vol = FALSE,
  od_specific_total_volume = NULL,
  odmeasure = NULL,
  odmeasure_conversion = NULL,
  plate_type = 96,
  outfolder = "."
)

Arguments

data_csv

path to a CSV file containing processed plate reader data

timecourse

logical. Is the data timecourse/kinetic data and does it include a variable called time?

flu_channels

the column names for the NORMALISED fluorescence data

flu_labels

the column names for the CALIBRATED fluorescence data

remove_wells

list of coordinates of wells to be removed from analysis (e.g. empty wells)

get_rfu_vol

logical. if TRUE, uses normalised_FP and OD-specific cell volume (od_specific_total_volume, specified in ul) to calculate FP concentration as FP/cellvolume in relative fluorescence units/litre (RFU/L).

get_mol_vol

logical. if TRUE, uses calibrated_FP and OD-specific cell volume (od_specific_total_volume, specified in ul) to calculate FP concentration as moles/L in Molar (M) units.

od_specific_total_volume

numeric. OD600-specific total cellular volume in ul x OD-1 x cm, i.e. the total cellular volume represented by 1 OD600 unit (in 1 cm path length). Recommended value is 3.6 from Volkmer et al., 2011.

odmeasure

character. Which OD measurement is being used in the data? Specifically, which measurement is represented by the 'normalised_OD_cm1' column? e.g. "OD600" or "OD700". Purpose is to record this in the table.

odmeasure_conversion

numeric. How to convert the measurement specified by odmeasure to OD600? i.e. OD600 = OD used / x. Use '1' for OD600 (no conversion) and 0.79 for OD700.

plate_type

type of plate. numeric, i.e. '96' for 96-well plate. Defines the rows and columns used for plotting figures. Defaults to '96'.

outfolder

path to folder where output files should be saved. Defaults to current working directory.

Value

a data.frame with columns for each FP/cell calculation

Examples

if (FALSE) {
conc_data_mCherry <- calc_fpconc(
  data_csv = "mcherry_parsed_processed.csv",
  flu_channels = c("red1red1"), flu_labels = c("mCherry"),
  remove_wells = c("A11"),
  get_rfu_vol = TRUE, get_mol_vol = TRUE,
  od_specific_total_volume = 3.6, odmeasure = "OD700", odmeasure_conversion = 0.79,
  outfolder = file.path("plots"))
}