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 3.0.2 Index]