Parse fluorimeter spectra
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")
)
A data frame with two columns:
Numeric. Number of seconds since the start of experiment.
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.
Path to a *.txt
file as a character
object.
A numeric
indicating the time
(in sec) at which fluorescence extrema are calculated (DEPENDENT ON
adjust
!).
A numeric
indicating the number of
data points used for extrema calculations.
A logical
indicating whether
(default) or not the timepoint of dithionite addition should be determined
using pracma-derived functionality.
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).
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.
Johannes Graumann
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).
scramblase_assay_input_validation
,
parse_felix_gx_output
,
parse_felix_32_output
,
parse_FluorS_Essence_3.8_output
,
parse_manual_output
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()
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