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.

Author
Gunnar Libiseller <Gunnar.Libiseller@joanneum.at>, Christoph Magnes <christoph.magnes@joanneum.at>
Date of publication
None
Maintainer
Thomas Riebenbauer <Thomas.Riebenbauer@joanneum.at>
License
GPL (>= 2) + file LICENSE
Version
1.0.0
URLs

View on Bioconductor

Man pages

attachList
Attaching one list at the end of another
calcPPS
Calculation of a peak picking score (PPS) by using natural,...
calculateXcmsSet
Calculation of an xcmsSet-Object
combineParams
Combining two lists of parameters together.
createModel
Creating a response surface model.
decode
En-/decodes values to/from ranges of -1 to 1.
findIsotopes.CAMERA
Identification of Isotopes using the package CAMERA.
findIsotopes.IPO
Identification of 13C isotopes
getBbdParameter
Creates a Box-Behnken Design of experiment
getCcdParameter
Creates a Central-Composite Design of experiment
getDefaultRetCorCenterSample
Gets the index of the sample with most peaks in it.
getDefaultRetGroupStartingParams
Gives a List of parameters for xcms-methods retcor.obiwarp or...
getDefaultXcmsSetStartingParams
Creates a List of parameters for xcms-methods...
getNormalizedResponse
It combines Retention time Correction Scores (RCS) and...
getRGTVValues
Calculation of values used for a Retention time correction...
IPO-package
Automated Optimization of Untargeted Metabolomics LC-MS Data...
optimizeRetGroup
Optimization for parameters for retention time correction and...
optimizeXcmsSet
Optimisation of peak picking parameters by using natural,...
toMatrix
Converts an array into a matrix
typeCastParams
Splits parameters into those which should be optimized and...
writeParamsTable
Writes XCMS settings to a file.
writeRScript
Prints an R-script to the screen which can be used for xcms...

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