do_groupChromPeaks_nearest: Core API function for chromatic peak grouping using a nearest...
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Value References See Also

View source: R/do_groupChromPeaks-functions.R

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).

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

`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.

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.

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

Other core peak grouping algorithms: do_groupChromPeaks_density(), do_groupPeaks_mzClust()

yclement/xcms documentation built on April 10, 2020, 12:08 a.m.