do_groupPeaks_mzClust: Core API function for peak grouping using mzClust

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Core API function for peak grouping using mzClust

Description

The do_groupPeaks_mzClust function performs high resolution correspondence on single spectra samples.

Usage

do_groupPeaks_mzClust(peaks, sampleGroups, ppm = 20, absMz = 0,
  minFraction = 0.5, minSamples = 1)

Arguments

peaks	A matrix or data.frame with the mz values and retention times of the identified chromatographic peaks in all samples of an experiment. Required columns are "mz", "rt" and "sample". The latter should contain numeric values representing the index of the sample in which the peak was found.
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).
ppm	numeric(1) representing the relative mz error for the clustering/grouping (in parts per million).
absMz	numeric(1) representing the absolute mz error for the clustering.
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).

Value

A list with elements "featureDefinitions" and "peakIndex". "featureDefinitions" is a matrix, each row representing an (mz-rt) feature (i.e. peak group) with columns:

• "mzmed": median of the peaks' apex mz values.

• "mzmin": smallest mz value of all peaks' apex within the feature.

• "mzmax": largest mz value of all peaks' apex within the feature.

• "rtmed": always -1.

• "rtmin": always -1.

• "rtmax": always -1.

• "npeaks": the total number of peaks assigned to the feature. Note that this number can be larger than the total number of samples, since multiple peaks from the same sample could be assigned to a group.

"peakIndex" is a list with the indices of all peaks in a peak group in the peaks input matrix.

References

Saira A. Kazmi, Samiran Ghosh, Dong-Guk Shin, Dennis W. Hill and David F. Grant
Alignment of high resolution mass spectra: development of a heuristic approach for metabolomics.
Metabolomics, Vol. 2, No. 2, 75-83 (2006)

See Also

Other core peak grouping algorithms: do_groupChromPeaks_density, do_groupChromPeaks_nearest

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.