Assess whether all the spectra in the list are not empty, of the same length and correspond to profile data.
Usage
check_spectra(spectra_list, tolerance = sqrt(.Machine$double.eps))Arguments
- spectra_list
A list of MALDIquant::MassSpectrum objects
- tolerance
A numeric indicating the accepted tolerance to the spectra length. The default value is the machine numerical precision and is close to 1.5e-8.
Value
A list of logical vectors of length spectra_list indicating if the spectra are empty (is_empty), of an odd length (is_outlier_length) or not a profile spectra (is_not_regular).
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 checks, with FALSE where no anomaly is detected
check_spectra(spectra_list)
#> $is_empty
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE
#>
#> $is_outlier_length
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE
#>
#> $is_not_regular
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE
#>
# The overall sanity can be checked with Reduce
Reduce(any, check_spectra(spectra_list)) # Should be FALSE
#> [1] FALSE