proFIA

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see proFIA.

Preprocessing of FIA-HRMS data


Bioconductor version: 3.11

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 outlook.fr>

Citation (from within R, enter citation("proFIA")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("proFIA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("proFIA")
processing FIA-HRMS data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software
Version 1.14.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License CeCILL
Depends R (>= 2.5.0), xcms
Imports stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls
System Requirements
URL
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Suggests BiocGenerics, plasFIA, knitr
Linking To
Enhances
Depends On Me plasFIA
Imports Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package proFIA_1.14.0.tar.gz
Windows Binary proFIA_1.14.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) proFIA_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/proFIA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/proFIA
Bioc Package Browser https://code.bioconductor.org/browse/proFIA/
Package Short Url https://bioconductor.org/packages/proFIA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive