import_biotyper_spectra: Importing spectra from the Bruker MALDI Biotyper device

In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

Importing spectra from the Bruker MALDI Biotyper device

Description

This function is a wrapper around the readBrukerFlexData::readBrukerFlexDir() to read both acqus and acqu MALDI files.

Usage

import_biotyper_spectra(
  biotyper_directory,
  remove_calibration = c("BTS", "Autocalibration")
)

Arguments

biotyper_directory	A path to the folder tree with the spectra to be imported.
remove_calibration	A vector of characters used as regex to indicate which (calibration) spectra are going to be removed.

Details

When using readBrukerFlexData::readBrukerFlexDir() on acqus files (instead of the native acqu files), the function will fail with the following error message:

Error in .readAcquFile(fidFile = fidFile, verbose = verbose) :
File ‘/data/maldi_dir/targetA/0_D10/1/1SLin/acqu’ doesn't exists!

But it turns out that acqu and acqus files are the same, so the function here create acqu symbolic links that point to acqus files.

Value

A list of MALDIquant::MassSpectrum objects

See Also

check_spectra, process_spectra

Examples

# Get an example directory of six Bruker MALDI Biotyper spectra
directory_biotyper_spectra <- system.file(
  "toy-species-spectra",
  package = "maldipickr"
)
# Import the six spectra
spectra_list <- import_biotyper_spectra(directory_biotyper_spectra)
# Display the list of spectra
spectra_list

maldipickr documentation built on Sept. 13, 2024, 1:12 a.m.