remove_spectra: Remove (raw or processed) spectra

In maldipickr: Dereplicate and Cherry-Pick Mass Spectrometry Spectra

Remove (raw or processed) spectra

Description

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.

Usage

remove_spectra(spectra_list, to_remove)

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_list or from check_spectra function. In the case of processed spectra: names of the spectra as formatted in get_spectra_names in the sanitized_name column.

Value

The same object as spectra_list minus the spectra in to_remove.

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(.))

# 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")

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