The remove_spectra() function is used to discard specific spectra from (1) raw spectra list by removing them, or (2) processed spectra by removing them from the spectra, peaks and metadata objects.
Arguments
- spectra_list
A list of MALDIquant::MassSpectrum objects OR A list of processed spectra from process_spectra
- to_remove
The spectra to be removed. In the case of raw spectra: a logical vector same size of
spectra_listor from check_spectra function. In the case of processed spectra: names of the spectra as formatted in get_spectra_names in thesanitized_namecolumn.
Examples
# Get an example directory of six Bruker MALDI Biotyper spectra
directory_biotyper_spectra <- system.file(
"toy-species-spectra",
package = "maldipickr"
)
# Import only the first two spectra
spectra_list <- import_biotyper_spectra(directory_biotyper_spectra)[1:2]
# Introduce artificially an empty raw spectra
spectra_list <- c(spectra_list, MALDIquant::createMassSpectrum(0, 0))
# Empty spectra are detected by `check_spectra()`
# and can be removed by `remove_spectra()`
spectra_list %>%
remove_spectra(to_remove = check_spectra(.))
#> Some spectra are incorrect (empty, outlier length or irregular).
#> They can be removed using `remove_spectra()`
#> [[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-4.4/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-4.4/x86_64-pc-linux-gnu/maldipickr/toy-species-spectra/species2/0_E11/1/1SLin/fid
#>
# Get an example processed spectra
processed_path <- system.file(
"three_processed_spectra_with_one_peakless.RDS",
package = "maldipickr")
processed <- readRDS(processed_path) %>% list()
# Remove a specific spectra
remove_spectra(processed, "empty_H12")
#> $spectra
#> $spectra$species1_G2
#> S4 class type : MassSpectrum
#> Number of m/z values : 7867
#> Range of m/z values : 4000.066 - 9999.46
#> Range of intensity values: 0e+00 - 2.181e-03
#> Memory usage : 133.625 KiB
#> Name : species1.G2
#> File : /maldipickr/inst/toy-species-spectra/species1/0_G2/1/1SLin/fid
#>
#> $spectra$species2_E11
#> S4 class type : MassSpectrum
#> Number of m/z values : 7867
#> Range of m/z values : 4000.066 - 9999.46
#> Range of intensity values: 0e+00 - 2.58e-03
#> Memory usage : 133.625 KiB
#> Name : species2.E11
#> File : /maldipickr/inst/toy-species-spectra/species2/0_E11/1/1SLin/fid
#>
#>
#> $peaks
#> $peaks$species1_G2
#> S4 class type : MassPeaks
#> Number of m/z values : 21
#> Range of m/z values : 4030.815 - 9989.171
#> Range of intensity values: 3.871e-04 - 2.181e-03
#> Range of snr values : 3.623 - 10.382
#> Memory usage : 11.352 KiB
#> Name : species1.G2
#> File : /maldipickr/inst/toy-species-spectra/species1/0_G2/1/1SLin/fid
#>
#> $peaks$species2_E11
#> S4 class type : MassPeaks
#> Number of m/z values : 22
#> Range of m/z values : 4031.408 - 9990.106
#> Range of intensity values: 2.034e-04 - 2.58e-03
#> Range of snr values : 3.14 - 11.027
#> Memory usage : 11.375 KiB
#> Name : species2.E11
#> File : /maldipickr/inst/toy-species-spectra/species2/0_E11/1/1SLin/fid
#>
#>
#> $metadata
#> # A tibble: 2 × 3
#> name SNR peaks
#> <chr> <dbl> <int>
#> 1 species1_G2 5.09 21
#> 2 species2_E11 5.54 22
#>