IPO

Automated Optimization of XCMS Data Processing parameters

Bioconductor version: Release (3.20)

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 Lieb <thomas.r.lieb at gmail.com>

Maintainer: Thomas Lieb <thomas.r.lieb at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version	1.32.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	GPL (>= 2) + file LICENSE
Depends	xcms(>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils
Imports	BiocParallel
System Requirements
URL	https://github.com/rietho/IPO
Bug Reports	https://github.com/rietho/IPO/issues/new

Suggests	RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
Linking To
Enhances	parallel
Depends On Me
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	IPO_1.32.0.tar.gz
Windows Binary (x86_64)	IPO_1.32.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/IPO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IPO
Bioc Package Browser	https://code.bioconductor.org/browse/IPO/
Package Short Url	https://bioconductor.org/packages/IPO/
Package Downloads Report	Download Stats