do_groupPeaks_mzClust {xcms} | R Documentation

## 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()`

[Package xcms version 3.10.2 Index]