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.

AuthorGunnar Libiseller <Gunnar.Libiseller@joanneum.at>, Christoph Magnes <christoph.magnes@joanneum.at>
Date of publicationNone
MaintainerThomas Riebenbauer <Thomas.Riebenbauer@joanneum.at>
LicenseGPL (>= 2) + file LICENSE
Version1.0.0
https://github.com/rietho/IPO

View on Bioconductor

Man pages

Files in this package

IPO/DESCRIPTION
IPO/LICENSE
IPO/NAMESPACE
IPO/R
IPO/R/IPO-internal.R IPO/R/optimizeRetCorGroupParameters.R IPO/R/optimizeXcmsSetParameters.R IPO/R/utils.R
IPO/README.md
IPO/build
IPO/build/vignette.rds
IPO/inst
IPO/inst/CITATION
IPO/inst/NEWS
IPO/inst/doc
IPO/inst/doc/IPO.R
IPO/inst/doc/IPO.Rmd
IPO/inst/doc/IPO.html
IPO/inst/unitTests
IPO/inst/unitTests/test_optimizeXcmsSet.R
IPO/man
IPO/man/IPO-package.Rd IPO/man/attachList.Rd IPO/man/calcPPS.Rd IPO/man/calculateXcmsSet.Rd IPO/man/combineParams.Rd IPO/man/createModel.Rd IPO/man/decode.Rd IPO/man/findIsotopes.CAMERA.Rd IPO/man/findIsotopes.IPO.Rd IPO/man/getBbdParameter.Rd IPO/man/getCcdParameter.Rd IPO/man/getDefaultRetCorCenterSample.Rd IPO/man/getDefaultRetGroupStartingParams.Rd IPO/man/getDefaultXcmsSetStartingParams.Rd IPO/man/getNormalizedResponse.Rd IPO/man/getRGTVValues.Rd IPO/man/optimizeRetGroup.Rd IPO/man/optimizeXcmsSet.Rd IPO/man/toMatrix.Rd IPO/man/typeCastParams.Rd IPO/man/writeParamsTable.Rd IPO/man/writeRScript.Rd
IPO/tests
IPO/tests/runTests.R
IPO/vignettes
IPO/vignettes/FlowChart.jpg
IPO/vignettes/IPO.Rmd
IPO/vignettes/rsmDirectory
IPO/vignettes/rsmDirectory/retgroup_rsm_1.jpg
IPO/vignettes/rsmDirectory/retgroup_rsm_2.jpg
IPO/vignettes/rsmDirectory/retgroup_rsm_3.jpg
IPO/vignettes/rsmDirectory/rsm_1.jpg
IPO/vignettes/rsmDirectory/rsm_2.jpg

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