Package: IPO 1.39.0

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]>

IPO_1.39.0.tar.gz
IPO_1.39.0.zip(r-4.7)IPO_1.39.0.zip(r-4.6)IPO_1.39.0.zip(r-4.5)
IPO_1.39.0.tgz(r-4.6-any)IPO_1.39.0.tgz(r-4.5-any)
IPO_1.39.0.tar.gz(r-4.7-any)IPO_1.39.0.tar.gz(r-4.6-any)
IPO_1.39.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
IPO/json (API)

# Install 'IPO' in R:

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

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

On BioConductor:IPO-1.39.0(bioc 3.24)IPO-1.38.0(bioc 3.23)

immunooncology metabolomics massspectrometry

8.20 score 34 stars 47 scripts 20 mentions 21 exports 151 dependencies

Last updated from:034338ee82. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	294
linux-devel-x86_64	NOTE	833
source / vignettes	OK	1065
linux-release-x86_64	NOTE	728
macos-release-arm64	NOTE	469
macos-oldrel-arm64	NOTE	577
windows-devel	NOTE	1218
windows-release	NOTE	1098
windows-oldrel	NOTE	1374
wasm-release	OK	259

Exports:attachList calcPPS calculateXcmsSet combineParams createModel decode decodeAll encode findIsotopes.CAMERA findIsotopes.IPO getBbdParameter getCcdParameter getDefaultRetGroupStartingParams getDefaultXcmsSetStartingParams getRGTVValues optimizeRetGroup optimizeXcmsSet toMatrix typeCastParams writeParamsTable writeRScript

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bslib cachem CAMERA checkmate cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest dir.expiry doParallel dplyr estimability evaluate farver fastmap filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomicRanges ggplot2 glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment mzID mzR ncdf4 nnet openssl otel pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch PTMods purrr QFeatures R6 rappdirs RBGL RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown rpart rsm rstudioapi S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite vsn withr xcms xfun XML XVector yaml

XCMS Parameter Optimization with IPO

Rendered fromIPO.Rmdusingknitr::rmarkdown

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

Help page	Topics
Automated Optimization of Untargeted Metabolomics LC-MS Data Processing	IPO-package IPO
Attaching one list at the end of another	attachList
Calculation of a peak picking score (PPS) by using natural, stable 13C isotopes	calcPPS
Calculation of an xcmsSet-Object	calculateXcmsSet
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 isotopes	findIsotopes.IPO
Creates a Box-Behnken Design of experiment	getBbdParameter
Creates a Central-Composite Design of experiment	getCcdParameter
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 default	getDefaultRetGroupStartingParams
Creates a List of parameters for xcms-methods xcmsSet.findPeak which are optimized by default	getDefaultXcmsSetStartingParams
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 grouping	optimizeRetGroup
Optimisation of peak picking parameters by using natural, stable 13C isotopes	optimizeXcmsSet
Converts an array into a matrix	toMatrix
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 processing	writeRScript

Package: IPO 1.39.0

IPO: Automated Optimization of XCMS Data Processing parameters

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