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Core API function for peak grouping using mzClust

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

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

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.

ppm

For MzClustParam: numeric(1) representing the relative m/z error for the clustering/grouping (in parts per million). For PeakDensityParam: numeric(1) to define m/z-dependent, increasing m/z bin sizes. If ppm = 0 (the default) m/z bins are defined by the sequence of values from the smallest to the larges m/z value with a constant bin size of binSize. For ppm > 0 the size of each bin is increased in addition by the ppm of the (upper) m/z boundary of the bin. The maximal bin size (used for the largest m/z values) would then be binSize plus ppm parts-per-million of the largest m/z value of all peaks in the data set.

absMz

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

minFraction

For PeakDensityParam: 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

For PeakDensityParam: 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()