optimizeXcmsSet: Optimisation of peak picking parameters by using natural,...
In IPO: Automated Optimization of XCMS Data Processing parameters

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/optimizeXcmsSetParameters.R

This function provides optimisation of peak picking parameters by using natural, stable 13C isotopes.

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optimizeXcmsSet(files, params = getDefaultXcmsSetStartingParams(),
  isotopeIdentification = c("IPO", "CAMERA"), BPPARAM = bpparam(), 
  nSlaves = 4, subdir = "IPO", plot = TRUE, ...)

`files`	A directory or list of files, passed to `xcmsSet`. If no files are given, xcmsSet() will check recursively all MS files in the current working directory.
`params`	A list of parameters which are needed by XCMS::findPeaks-Methods. List-items with two values will be optimized. The first value defines the lower test value, the second one the higher test value.
`isotopeIdentification`	This parameter defines the method for isotope identification. The method 'IPO' was especially implemented for high resolution data. CAMERA is an established isotope and adduct annotation package.
`BPPARAM`	a `BiocParallel` parameter object to control how and if parallel processing of `xcmsSet` should be performed. Such objects can be created by the `SerialParam`, `MulticoreParam` or `SnowParam` functions. Note: `xcmsSet`'s `nSlaves`-argument is deprecated.
`nSlaves`	Number of slaves the optimization process should spawn.
`subdir`	The name of the subdirectory which is created and where the figures of the response surface models will be saved to. `NULL` plots the figures to the graphic device. This parameter is ignored, if `plot = TRUE`.
`plot`	Defines if plots should be generated (`TRUE`) or not (`FALSE`). This parameter overwrites the `subdir`-parameter. Defaults to `TRUE`.
`...`	Additional parameters to CAMERA's or IPO's findIsotopes functions

This function provides optimisation of peak picking parameters by using natural, stable 13C isotopes.

A LIST of length n+1 with n beeing the optimization runs (DoEs) needed

comp1-comp(n)

A LIST containing:
1. Parameters used for the nth optimization run
2. Box-Behnken or Central Composite Design used for optimization run
3. Responses from calcPPS for every experiment in the design
4. Response surface model for the design
5. The normalized parameter settings giving the best PPS (values between -1 and 1) 6. an xcmsSet-class-object calculated with the best settings from the response surface model 7. PPS calculated from the xcmsSet

comp(n+1)

A LIST containing:
1. Parameters giving the best PPS
2. An xcmsSet-object created with the optimized parameters
3. The result of calcPPS() of the xcmsSet created with the best parameters

Gunnar Libiseller, Thomas Riebenbauer (thomas.riebenbauer@joanneum.at)

Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)

Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)

H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels: Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)

C. Kuhl and R. Tautenhahn and C. Boettcher and T. R. Larson and S. Neumann: CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets Analytical Chemistry 84:283 (2012)

getDefaultXcmsSetStartingParams, calcPPS, findIsotopes.IPO, findIsotopes.CAMERA

#library(IPO)
 
mzmlfile <- file.path(find.package("msdata"), "microtofq/MM14.mzML")
 
paramsPP <- getDefaultXcmsSetStartingParams()
paramsPP$mzdiff <- -0.001
paramsPP$min_peakwidth <- c(7,14)
paramsPP$max_peakwidth <- c(20,30)
#example using IPO isotope identification
resultPP <- optimizeXcmsSet(mzmlfile, paramsPP, subdir="mtbls2")

#example using CAMERA isotope identification
resultPP <- optimizeXcmsSet(mzmlfile, paramsPP, isotopeIdentification="CAMERA", 
                            subdir="mtbls2", ppm=15, maxcharge=2)