DOI: 10.18129/B9.bioc.proFIA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see proFIA.

Preprocessing of FIA-HRMS data

Bioconductor version: 3.16

Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and generate the peak table. The workflow includes noise modelling, band detection and filtering then signal matching and missing value imputation. The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.

Author: Alexis Delabriere and Etienne Thevenot.

Maintainer: Alexis Delabriere <alexis.delabriere at>

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biocViews Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software
Version 1.23.0
In Bioconductor since BioC 3.4 (R-3.3) (6.5 years)
License CeCILL
Depends R (>= 2.5.0), xcms
Imports stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls
Suggests BiocGenerics, plasFIA, knitr
Depends On Me plasFIA
Imports Me
Suggests Me
Links To Me
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