parse_fluorimeter_output
parse_fluorimeter_output
Parse fluorimeter spectra
Usage
parse_fluorimeter_output(spec_file = NULL, adjust = TRUE,
file_type = c("auto", "FelixGXv4.1.0.3096", "Felix32v1.20", "manual"))Arguments
- spec_file
- Path to a
*.txtfile as acharacterobject. - adjust
- A
logicalindicating of whether (default) or not acquisition time should be reset to have0(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 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) and Felix32 v1.20 (see
parse_felix_32_output). 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 wmtsa-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).
WavelengthsInNanometres, which contains the
excitation and emission wavelengths.
See Also
scramblase_assay_input_validation,
parse_felix_gx_output,
parse_felix_32_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) %>%
str()