IPO

DOI: 10.18129/B9.bioc.IPO    

Automated Optimization of XCMS Data Processing parameters

Bioconductor version: Release (3.15)

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.

Author: Gunnar Libiseller <Gunnar.Libiseller at joanneum.at>, Christoph Magnes <christoph.magnes at joanneum.at>, Thomas Riebenbauer <Thomas.Riebenbauer at joanneum.at>

Maintainer: Thomas Riebenbauer <Thomas.Riebenbauer at joanneum.at>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IPO")

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("IPO")

 

HTML	R Script	XCMS Parameter Optimization with IPO
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.22.1
In Bioconductor since	BioC 3.4 (R-3.3) (6 years)
License	GPL (>= 2) + file LICENSE
Depends	xcms(>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils
Imports	BiocParallel
LinkingTo
Suggests	RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
SystemRequirements
Enhances	parallel
URL	https://github.com/rietho/IPO
BugReports	https://github.com/rietho/IPO/issues/new
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	IPO_1.22.1.tar.gz
Windows Binary	IPO_1.22.1.zip (64-bit only)
macOS Binary (x86_64)	IPO_1.22.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IPO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IPO
Package Short Url	https://bioconductor.org/packages/IPO/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive