proFIA

DOI: 10.18129/B9.bioc.proFIA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see proFIA.

Preprocessing of FIA-HRMS data

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	processing FIA-HRMS data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software
Version	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	CeCILL
Depends	R (>= 2.5.0), xcms
Imports	stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls
LinkingTo
Suggests	BiocGenerics, plasFIA, knitr
SystemRequirements
Enhances
URL
Depends On Me	plasFIA
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	proFIA_1.10.0.tar.gz
Windows Binary	proFIA_1.10.0.zip
Mac OS X 10.11 (El Capitan)	proFIA_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/proFIA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/proFIA
Package Short Url	https://bioconductor.org/packages/proFIA/
Package Downloads Report	Download Stats