do_groupChromPeaks_nearest {xcms} | R Documentation

## Core API function for chromatic peak grouping using a nearest neighbor approach

### Description

The `do_groupChromPeaks_nearest` function groups peaks across samples by creating a master peak list and assigning corresponding peaks from all samples to each peak group (i.e. feature). The method is inspired by the correspondence algorithm of mzMine (Katajamaa 2006).

### Usage

    do_groupChromPeaks_nearest(peaks, sampleGroups, mzVsRtBalance = 10,
      absMz = 0.2, absRt = 15, kNN = 10)

### 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).
`mzVsRtBalance` | `numeric(1)` representing the factor by which mz values are multiplied before calculating the (euclician) distance between two peaks.
`absMz` | `numeric(1)` maximum tolerated distance for mz values.
`absRt` | `numeric(1)` maximum tolerated distance for rt values.
`kNN` | `numeric(1)` representing the number of nearest neighbors to check.

### 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"`: the median of the peaks' retention times.

- `"rtmin"`: the smallest retention time of the peaks in the feature.

- `"rtmax"`: the largest retention time of the peaks in the feature.

- `"npeaks"`: the total number of peaks assigned to the feature.

`"peakIndex"` is a `list` with the indices of all peaks in a feature in the `peaks` input matrix.

### References

Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22:634-636.

### See Also

Other core peak grouping algorithms: `do_groupChromPeaks_density`, `do_groupPeaks_mzClust`

[Package xcms version 3.6.2 Index]