rMSIproc: an R package for mass spectrometry imaging data processing
Pere Ràfols, Bram Heijs, Esteban del Castillo, Óscar Yanes, Liam A. McDonnell, J. Brezmes, Iara Pérez‐Taboada, Mario Vallejo, María García‐Altares, Xavier Correig
Abstract
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: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.