To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IPO")

In most cases, you don't need to download the package archive at all.

IPO

DOI: 10.18129/B9.bioc.IPO    

This is the development version of IPO; for the stable release version, see IPO.

Automated Optimization of XCMS Data Processing parameters

Bioconductor version: Development (3.7)

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IPO")

Documentation

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

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.5.1
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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
Build Report  

Package Archives

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

Source Package IPO_1.5.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) IPO_1.5.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/IPO
Package Short Url http://bioconductor.org/packages/IPO/
Package Downloads Report Download Stats

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