To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("proFIA")

In most cases, you don't need to download the package archive at all.

proFIA

DOI: 10.18129/B9.bioc.proFIA    

Preprocessing of FIA-HRMS data

Bioconductor version: Release (3.5)

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 cea.fr>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("proFIA")

Documentation

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

Details

biocViews Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License CeCILL
Depends R (>= 3.3.0), xcms
Imports stats, graphics, utils, grDevices, methods, pracma, maxLik, Biobase, FNN, minpack.lm, BiocParallel, ropls
LinkingTo
Suggests BiocGenerics, plasFIA, knitr
SystemRequirements
Enhances
URL
Depends On Me plasFIA
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source proFIA_1.2.0.tar.gz
Windows Binary proFIA_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) proFIA_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/proFIA
Package Short Url http://bioconductor.org/packages/proFIA/
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