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)
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files |
a vector containing the files for peak picking |
xcmsSetParameters |
a list with all parameters for |
scanrange |
scan range to process. See |
task |
The task-id when using this method in parallel calculations. |
BPPARAM |
a |
nSlaves |
|
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)
1 2 3 4 5 6 7 8 | 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)
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