Importing spectra from the Bruker MALDI Biotyper device
Source:R/import_biotyper_spectra.R
import_biotyper_spectra.RdThis 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.
Value
A list of MALDIquant::MassSpectrum objects
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.
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
#> [[1]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1962.222 - 20146.522
#> Range of intensity values: 2.4e+02 - 3.608e+04
#> Memory usage : 337.062 KiB
#> Name : species1.G2
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species1/0_G2/1/1SLin/fid
#>
#> [[2]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1962.222 - 20146.522
#> Range of intensity values: 1.82e+02 - 1.006e+04
#> Memory usage : 337.062 KiB
#> Name : species2.E11
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species2/0_E11/1/1SLin/fid
#>
#> [[3]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1962.222 - 20146.522
#> Range of intensity values: 3.25e+02 - 2.115e+04
#> Memory usage : 337.062 KiB
#> Name : species2.E12
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species2/0_E12/1/1SLin/fid
#>
#> [[4]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1961.215 - 20135.904
#> Range of intensity values: 1.94e+02 - 2.055e+04
#> Memory usage : 337.062 KiB
#> Name : species3.F7
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species3/0_F7/1/1SLin/fid
#>
#> [[5]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1961.215 - 20135.904
#> Range of intensity values: 1.6e+02 - 1.814e+04
#> Memory usage : 337.062 KiB
#> Name : species3.F8
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species3/0_F8/1/1SLin/fid
#>
#> [[6]]
#> S4 class type : MassSpectrum
#> Number of m/z values : 20882
#> Range of m/z values : 1961.215 - 20135.904
#> Range of intensity values: 1.59e+02 - 1.449e+04
#> Memory usage : 337.062 KiB
#> Name : species3.F9
#> File : /home/runner/.cache/R/renv/library/maldipickr-8ce40efa/R-4.3/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species3/0_F9/1/1SLin/fid
#>