Package: proFIA
Type: Package
Title: Preprocessing of FIA-HRMS data
Version: 1.0.10
Date: 2016-05-04
Author: Alexis Delabriere and Etienne Thevenot.
Maintainer: Alexis Delabriere <alexis.delabriere@cea.fr>
biocViews: MassSpectrometry, Metabolomics, Lipidomics, Preprocessing,
        PeakDetection, Proteomics
Depends: R (>= 3.3.0), xcms
Imports: stats, graphics, utils, grDevices, methods, pracma, Biobase,
        FNN, minpack.lm, BiocParallel
Suggests: ropls, BiocGenerics, plasFIA, knitr,
VignetteBuilder: knitr
Description: 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.
License: CeCILL
NeedsCompilation: yes
RoxygenNote: 5.0.1
Collate: 'Denoising.R' 'cWrapper.R' 'noiseEstimator.R'
        'classContainer.R' 'fastMatchPpm.R' 'findPeaksFIA.R'
        'methodsContainer.R' 'proFIA-package.R'
Packaged: 2016-10-29 00:34:58 UTC; biocbuild
Built: R 3.3.1; i386-w64-mingw32; 2016-10-29 03:59:27 UTC; windows
Archs: i386, x64
