calculateXcmsSet: Calculation of an xcmsSet-Object

In glibiseller/IPO: Automated Optimization of XCMS Data Processing parameters

Calculation of an xcmsSet-Object

Description

This function encapsulates xcms::findPeaks-methods for IPO

Usage

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

Arguments

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.

Details

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

Value

An xcmsSet-object

Author(s)

Gunnar Libiseller, Thomas Riebenbauer ([e-mail])

References

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)

See Also

findPeaks

Examples

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)

glibiseller/IPO documentation built on Dec. 4, 2022, 7:09 a.m.