IPO: Automated Optimization of XCMS Data Processing parameters

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("IPO")
AuthorGunnar Libiseller <Gunnar.Libiseller@joanneum.at>, Christoph Magnes <christoph.magnes@joanneum.at>, Thomas Riebenbauer <Thomas.Riebenbauer@joanneum.at>
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerThomas Riebenbauer <Thomas.Riebenbauer@joanneum.at>
LicenseGPL (>= 2) + file LICENSE
Version1.2.0
https://github.com/rietho/IPO

View on Bioconductor

Man pages

Functions

attachList Man page
calcPPS Man page
calculateXcmsSet Man page
combineParams Man page
createModel Man page
decode Man page
decodeAll Man page
encode Man page
findIsotopes.CAMERA Man page
findIsotopes.IPO Man page
getBbdParameter Man page
getCcdParameter Man page
getDefaultRetCorCenterSample Man page
getDefaultRetGroupStartingParams Man page
getDefaultXcmsSetStartingParams Man page
getNormalizedResponse Man page
getRGTVValues Man page
IPO Man page
IPO-package Man page
optimizeRetGroup Man page
optimizeXcmsSet Man page
toMatrix Man page
typeCastParams Man page
writeParamsTable Man page
writeRScript Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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