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

Source: R/do_groupChromPeaks-functions.R
do_groupChromPeaks_nearest.Rd

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

For PeakDensityParam: 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 PeakDensityParam and has to be defined also if there is no sample grouping in the experiment (in which case all samples should be assigned to the same group). Samples for which a NA is provided will not be considered in the feature definitions step. Providing NA for all blanks in an experiment will for example avoid features to be defined for signals (chrom peaks) present only in blank samples.

mzVsRtBalance

For NearestPeaksParam: numeric(1) representing the factor by which m/z values are multiplied before calculating the (euclician) distance between two peaks.

absMz

For NearestPeaksParam and MzClustParam: numeric(1) maximum tolerated distance for m/z values.

absRt

For NearestPeaksParam: numeric(1) maximum tolerated distance for retention times.

kNN

For NearestPeaksParam: integer(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()