do_groupPeaks_mzClust: Core API function for peak grouping using mzClust

Description Usage Arguments Value References See Also

View source: R/do_groupChromPeaks-functions.R

Description

The do_groupPeaks_mzClust function performs high resolution correspondence on single spectra samples.

Usage

1
2

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).

ppm

numeric(1) representing the relative mz error for the clustering/grouping (in parts per million).

absMz

numeric(1) representing the absolute mz error for the clustering.

minFraction

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

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:

"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


xcms documentation built on May 18, 2019, 2 a.m.