rMSIproc: an R package for mass spectrometry imaging data processing

Identifier:  imarina:6406026

Handle: https://hdl.handle.net/20.500.11797/imarina6406026

Authors:  Rafols, Pere; Heijs, Bram; del Castillo, Esteban; Yanes, Oscar; McDonnell, Liam A; Brezmes, Jesus; Perez-Taboada, Iara; Vallejo, Mario; Garcia-Altares, Maria; Correig, Xavier

Abstract:
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. SUMMARY: Mass spectrometry imaging (MSI) can reveal biochemical information directly from a tissue section. MSI generates a large quantity of complex spectral data which is still challenging to translate into relevant biochemical information. Here, we present rMSIproc, an open-source R package that implements a full data processing workflow for MSI experiments performed using TOF or FT-based mass spectrometers. The package provides a novel strategy for spectral alignment and recalibration, which allows to process multiple datasets simultaneously. This enables to perform a confident statistical analysis with multiple datasets from one or several experiments. rMSIproc is designed to work with files larger than the computer memory capacity and the algorithms are implemented using a multi-threading strategy. rMSIproc is a powerful tool able to take full advantage of modern computer systems to completely develop the whole MSI potential. AVAILABILITY AND IMPLEMENTATION: rMSIproc is freely available at https://github.com/prafols/rMSIproc. CONTACT: pere.rafols@urv.cat. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.