PeakDensityPar: Peak density parameters

In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description

The method creates a template with the parameters for correspondence. Extracted from the function xcms::PeakDensityParam.

Usage

PeakDensityPar(...)

Arguments

...

Arguments passed on to xcms::PeakDensityParam sampleGroups A vector of the same length than samples defining the sample group assignments (i.e. which samples belong to which sample group). This parameter is mandatory for the PeakDensityParam and has to be provided also if there is no sample grouping in the experiment (in which case all samples should be assigned to the same group). bw numeric(1) defining the bandwidth (standard deviation ot the smoothing kernel) to be used. This argument is passed to the [density() method. minFraction numeric(1) defining the minimum fraction of samples in at least one sample group in which the peaks have to be present to be considered as a peak group (feature). minSamples numeric(1) with the minimum number of samples in at least one sample group in which the peaks have to be detected to be considered a peak group (feature). binSize numeric(1) defining the size of the overlapping slices in mz dimension. maxFeatures numeric(1) with the maximum number of peak groups to be identified in a single mz slice.

Value

PeakDensityParam S4 object

Slots

.__classVersion__,sampleGroups,bw,minFraction,minSamples,binSize,maxFeatures

See corresponding parameter above. .__classVersion__ stores the version from the class. Slots values should exclusively be accessed via the corresponding getter and setter methods listed above.

Author(s)

Colin Smith, Johannes Rainer

References

Colin A. Smith, Elizabeth J. Want, Grace O'Maille, Ruben Abagyan and Gary Siuzdak. "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification" Anal. Chem. 2006, 78:779-787.

See Also

The do_groupChromPeaks_density() core API function and group.density() for the old user interface.

plotChromPeakDensity() to plot peak densities and evaluate different algorithm settings.

featureDefinitions() and featureValues() for methods to access the features (i.e. the peak grouping results).

XCMSnExp for the object containing the results of the correspondence.

plotChromPeakDensity() for plotting chromatographic peak density with the possibility to test different parameter settings.

Other peak grouping methods: groupChromPeaks-mzClust, groupChromPeaks-nearest, groupChromPeaks()

Examples

p <- PeakDensityPar(sampleGroups = c(1,2))

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.