proFIA
This package is for version 3.9 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: 3.9
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>
citation("proFIA")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software |
| Version | 1.10.0 |
| 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 |
See More
| Suggests | BiocGenerics, plasFIA, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | plasFIA |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 3.9 | Source Archive |