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
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see proFIA.
Preprocessing of FIA-HRMS data
Bioconductor version: 3.4
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 | Vignette Title |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Lipidomics, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Proteomics, Software |
| Version | 1.0.10 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
| License | CeCILL |
| Depends | R (>= 3.3.0), xcms |
| Imports | stats, graphics, utils, grDevices, methods, pracma, Biobase, FNN, minpack.lm, BiocParallel |
| LinkingTo | |
| Suggests | ropls, 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_1.0.10.tar.gz |
| Windows Binary | proFIA_1.0.10.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | proFIA_1.0.10.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/proFIA/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/proFIA/ |
| Package Downloads Report | Download Stats |
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