parse_fluorimeter_output {flippant}

parse_fluorimeter_output

Description

Parse fluorimeter spectra

Usage

parse_fluorimeter_output(
  spec_file = NULL,
  timepoint_of_measurement = NULL,
  n_averaging = 10,
  determine_zero_time = TRUE,
  adjust = TRUE,
  file_type = c("auto", "FelixGXv4.1.0.3096", "Felix32v1.20", "FluorSEssencev3.8",
    "manual")
)

Arguments

spec_file

Path to a ‘*.txt’ file as a character object.

timepoint_of_measurement

A numeric indicating the time (in sec) at which fluorescence extrema are calculated (DEPENDENT ON adjust!).

n_averaging

A numeric indicating the number of data points used for extrema calculations.

determine_zero_time

A logical indicating whether (default) or not the timepoint of dithionite addition should be determined using pracma-derived functionality.

adjust

A logical indicating of whether (default) or not acquisition time should be reset to have 0 (zero) coincide with the addition of dithionite (see 'Details' section).

file_type

A string specifying whether or the file was created using Felix GX or Felix 32 or FluorS Essence v3.8 or is a "manual" tab delimited file.

Details

A function to read fluorimeter output directly. Intended as a helper function to scramblase activity determinations from dithionite assays.

The function is currently capable to deal with input derived from QuantaMaster instruments (Photon Technology International, Inc., Edison, New Jersey)running software versions FelixGX v4.1 (see parse_felix_gx_output), Felix32 v1.20 (see parse_felix_32_output) as well as Horiba fluorimeters (HORIBA Europe GmbH, Oberursel, Germany) using FluorS Essence v3.8. The format used in a given file is divined from the data structure and appropriate internal parsing functions are called.

If requested the time point of dithionite addition to a sample is determined using pracma-supplied methodology and the acquisition time reset accordingly (0 henceforth corresponds to the time of addition).

Value

A data frame with two columns:

Time.in.sec

Numeric. Number of seconds since the start of experiment.

Fluorescence.Intensity

Numeric. Intensity of fluorescence (relative scale, no official unit).

If determine_zero_time and/or adjust are set to TRUE, the return value will have an attribute ZeroTimePoint corresponding to the determined time point of dithionite addition (always 0 (zero) where adjust == TRUE).

For Felix GX, if the file contains the information, the return value will also have an attribute WavelengthsInNanometres, which contains the excitation and emission wavelengths.

Author(s)

Johannes Graumann

See Also

scramblase_assay_input_validation, parse_felix_gx_output, parse_felix_32_output, parse_FluorS_Essence_3.8_output, parse_manual_output

Examples

library(magrittr)
# Extract example data
analysis_dir <- file.path(tempdir(), "flippant-case-study")
fluor_file <- extract_case_study_data(analysis_dir, "wildtypeEx1_0.txt")
# Parse an exemplary file
parse_fluorimeter_output(fluor_file, timepoint_of_measurement = 350) %>%
  str()