Package: IPO 1.33.0

Thomas Lieb

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.

Authors:Gunnar Libiseller <[email protected]>, Christoph Magnes <[email protected]>, Thomas Lieb <[email protected]>

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IPO.pdf |IPO.html✨
IPO/json (API)
NEWS

# Install 'IPO' in R:
install.packages('IPO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/rietho/ipo/issues

On BioConductor:IPO-1.33.0(bioc 3.21)IPO-1.32.0(bioc 3.20)

immunooncologymetabolomicsmassspectrometry

8.13 score 34 stars 40 scripts 439 downloads 20 mentions 21 exports 153 dependencies

Last updated 23 days agofrom:6da5785401. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:attachListcalcPPScalculateXcmsSetcombineParamscreateModeldecodedecodeAllencodefindIsotopes.CAMERAfindIsotopes.IPOgetBbdParametergetCcdParametergetDefaultRetGroupStartingParamsgetDefaultXcmsSetStartingParamsgetRGTVValuesoptimizeRetGroupoptimizeXcmsSettoMatrixtypeCastParamswriteParamsTablewriteRScript

Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemCAMERAcheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrestimabilityevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrsmrstudioapiS4ArraysS4VectorssassscalessnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc

XCMS Parameter Optimization with IPO

Gunnar Libiseller, Thomas RiebenbauerJOANNEUM RESEARCH Forschungsgesellschaft m.b.H., Graz, Austria

Rendered fromIPO.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-06-30
Started: 2016-07-22

Readme and manuals

Help Manual

Help pageTopics
Automated Optimization of Untargeted Metabolomics LC-MS Data ProcessingIPO-package IPO
Attaching one list at the end of anotherattachList
Calculation of a peak picking score (PPS) by using natural, stable 13C isotopescalcPPS
Calculation of an xcmsSet-ObjectcalculateXcmsSet
Combining two lists of parameters together.combineParams
Creating a response surface model.createModel
En-/decodes values to/from ranges of -1 to 1.decode decodeAll encode
Identification of Isotopes using the package CAMERA.findIsotopes.CAMERA
Identification of 13C isotopesfindIsotopes.IPO
Creates a Box-Behnken Design of experimentgetBbdParameter
Creates a Central-Composite Design of experimentgetCcdParameter
Gets the index of the sample with most peaks in it.getDefaultRetCorCenterSample
Gives a List of parameters for xcms-methods retcor.obiwarp or retcor.loess and group.density which are optimized by defaultgetDefaultRetGroupStartingParams
Creates a List of parameters for xcms-methods xcmsSet.findPeak which are optimized by defaultgetDefaultXcmsSetStartingParams
It combines Retention time Correction Scores (RCS) and Grouping Scores (GS)getNormalizedResponse
Calculation of values used for a Retention time correction and Grouping Target Value (RGTV)getRGTVValues
Optimization for parameters for retention time correction and groupingoptimizeRetGroup
Optimisation of peak picking parameters by using natural, stable 13C isotopesoptimizeXcmsSet
Converts an array into a matrixtoMatrix
Splits parameters into those which should be optimized and those which are fixed.typeCastParams
Writes XCMS settings to a file.writeParamsTable
Prints an R-script to the screen which can be used for xcms processingwriteRScript