calculateXcmsSet: Calculation of an xcmsSet-Object
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 encapsulates xcms::findPeaks-methods for IPO

1 2	calculateXcmsSet(files, xcmsSetParameters, scanrange=NULL, task=1, BPPARAM = bpparam(), nSlaves=0)

`files`	a vector containing the files for peak picking
`xcmsSetParameters`	a list with all parameters for `xcmsSet`-methods as list-items
`scanrange`	scan range to process. See `findPeaks.centWave`.
`task`	The task-id when using this method in parallel calculations.
`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.
`nSlaves`	`xcmsSet`'s `nSlaves`-argument is deprecated., use `BPPARAM` argument instead.

Encapsulation of xcms::findPeaks-methods used in IPO.

An xcmsSet-object

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)

findPeaks

mzmlfile <- file.path(find.package("msdata"), "microtofq/MM14.mzML")

params <- list(min_peakwidth=5, max_peakwidth=12, ppm=58,
                  mzdiff=-0.001, snthresh=10, noise=0, prefilter=3, 
                  value_of_prefilter=100,  mzCenterFun="wMean", integrate=1, 
                  fitgauss=FALSE, verbose.columns=FALSE, nSlaves=1)

xset <- calculateXcmsSet(mzmlfile, params)