calc_fpconc.Rd
Takes as input timecourse 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 df.
calc_fpconc( data_csv, flu_channels, flu_labels, remove_wells, get_rfu_vol = TRUE, get_mol_vol = FALSE, od_specific_total_volume = NULL, odmeasure = NULL, odmeasure_conversion = NULL, outfolder = "." )
data_csv | path to a csv file containing processed plate reader data |
---|---|
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 (eg. empty wells) |
get_rfu_vol | logical. if TRUE, uses normalised_FP and OD-specific cell
volume ( |
get_mol_vol | logical. if TRUE, uses calibrated_FP and OD-specific cell
volume ( |
od_specific_total_volume | numeric. OD600-specific total cellular volume in ulOD-1cm, ie. 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? eg. "OD600" or "OD700". Purpose is to record this in the table. |
odmeasure_conversion | numeric. How to convert the measurement specified by odmeasure to OD600? ie. OD600 = ODused / x. Use '1' for OD600 (no conversion) and 0.79 for OD700. |
outfolder | path to folder where output files should be saved. Defaults to current working directory. |
a data.frame with columns for each FP/cell calculation
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"))