Package index • maldipickr

Import

Functions to import raw spectra, identifications or clusters

import_biotyper_spectra(): Importing spectra from the Bruker MALDI Biotyper device

import_spede_clusters(): Import clusters results generated by SPeDE

read_biotyper_report(): Importing Bruker MALDI Biotyper CSV report

read_many_biotyper_reports(): Importing a list of Bruker MALDI Biotyper CSV reports

Process

Functions to analyze and verify multiple spectra data

check_spectra(): Evaluate the spectra regularities

merge_processed_spectra(): Merge multiple processed spectra and peaks

process_spectra(): Process Bruker MALDI Biotyper spectra à la Strejcek et al. (2018)

remove_spectra(): Remove (raw or processed) spectra

Dereplicate

Functions to cluster and reduce redundancy

delineate_with_identification(): Delineate clusters from taxonomic identifications

delineate_with_similarity(): Delineate clusters from a similarity matrix

Cherry-pick

Function to pinpoint and label specific spectra within clusters

pick_spectra(): Cherry-pick Bruker MALDI Biotyper spectra

set_reference_spectra(): Set a reference spectrum for each cluster

Miscellaneous

is_well_on_edge(): Identify the wells on the plate's edge

gather_spectra_stats(): Aggregate spectra quality-check statistics

get_spectra_names(): Extract spectra names and check for uniqueness