Process and correct excitation–emission matrices (EEMs)

Wrapper function that combines multiple EEM processing steps into a streamlined workflow. The processing steps include:

subtract_blank(): subtracts blank samples from the EEMs
remove_scattering(): removes scattering lines with optional interpolation
ife_correct(): corrects for inner filter effects
raman_normalize(): normalizes fluorescence intensity to Raman units
correct_dilution(): adjusts intensity for sample dilutions
eemR::eem_cut(): clips the excitation–emission matrices to the region of interest

Usage

process_eem(
  eemlist,
  abslist,
  ex_clip = c(247, 450),
  em_clip = c(247, 600),
  type = c(TRUE, TRUE, TRUE, TRUE),
  width = c(16, 3, 30, 10),
  interpolate = c(TRUE, TRUE, FALSE, FALSE),
  method = 1,
  cores = 1,
  cuvle = 1
)

Arguments

eemlist: An eemlist object.
abslist: An abslist object.
ex_clip: Numeric vector of length two specifying the minimum and maximum excitation wavelengths to keep.
em_clip: Numeric vector of length two specifying the minimum and maximum emission wavelengths to keep.
type: Logical vector of length four indicating which scattering lines to remove. The order is "raman1", "raman2", "rayleigh1", "rayleigh2".
width: Numeric vector of length four specifying the width of scattering lines to remove (nm). Same order as type.
interpolate: Logical vector of length four indicating which scattering lines to interpolate. Same order as type.
method: Numeric (0–4) specifying the interpolation method to use. Default is 1. See staRdom::eem_interp() for details.
cores: Integer specifying the number of cores for parallel computation during interpolation.
cuvle: Cuvette (path) length in cm.

Value

An eemlist object with processed and corrected EEMs.

Details

Metadata

Absorbance and EEM data are linked via the meta_name in the metadata. Metadata must already be added to the samples using add_metadata().

Tracking Processing Steps

Processing steps are tracked in two ways:

Each sample has an attribute that records its processing steps. You can view this using attributes(eem).
Overall processing steps are recorded in a readme variable (accessible using print_readme()) or exported as the readme.txt file using export_data().

Examples

eemlist <- add_metadata(metadata, example_eems)
abslist <- add_metadata(metadata, example_abs)
blanklist <- subset_type(eemlist, "iblank")
eemlist <- add_blanks(eemlist, blanklist)
corrected_eem <- process_eem(eemlist, abslist)
plot(corrected_eem)