IPO
Automated Optimization of XCMS Data Processing parameters
Bioconductor version: 3.24 · Package version: 1.39.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.
DOI: 10.18129/B9.bioc.IPO
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IPO")Details
| Maintainer | Thomas Lieb <thomas.r.lieb@gmail.com> |
| Author | Gunnar Libiseller <Gunnar.Libiseller@joanneum.at>, Christoph Magnes <christoph.magnes@joanneum.at>, Thomas Lieb <thomas.r.lieb@gmail.com> |
| License | GPL (>= 2) + file LICENSE |
| URL | https://github.com/rietho/IPO |
| Bug Reports | https://github.com/rietho/IPO/issues/new |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software |
| Package Short Url | https://bioconductor.org/packages/IPO/ |
Citation
From within R, enter citation("IPO"):
Gunnar Libiseller, Christoph Magnes, Thomas Lieb. IPO: Automated Optimization of XCMS Data Processing parameters. doi:10.18129/B9.bioc.IPO, R package version 1.39.0, https://bioconductor.org/packages/IPO.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | IPO_1.39.0.tar.gz |
| Windows binary (x86_64) | IPO_1.39.0.zip |
| macOS binary (arm64) | IPO_1.39.0.tgz |
| macOS binary (x86_64) | IPO_1.39.0.tgz |
Dependencies
Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils
Imports: BiocParallel
Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
Enhances: parallel