Description: Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element
isotopes, calculating exact monoisitopic mass, m/z values and mass accuracy, inspecting possible contaminant mass peaks,
examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI)
ion sources, and calculating chemical similarities.

isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks,

Imports: stringr, crayon, xml2, magrittr, ropls, stats, reshape2,

Imports: stringr, crayon, xml2, stats, reshape2, ggplot2, ggfortify,

Title: Automated Classification of Mass Spectra
person("Alexandre", "Godmer", role=c("aut", "cre"), email="alexandre.godmer@aphp.fr"),
Description: Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values.
Imports: e1071, MALDIquant, MALDIrppa, MALDIquantForeign, mixOmics,
caret, reshape2, ggplot2, nnet, dplyr, fuzzyjoin, VSURF, metap,

Description: Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values. Two vignettes illustrating how to use the functions of this package from real data sets are also available online to help users: <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Ecrobia.html> and <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Klebsiella.html>.