chromPeakSummary: Chromatographic peak summaries

In sneumann/xcms: LC-MS and GC-MS Data Analysis

Chromatographic peak summaries

Description

The chromPeakSummary() method calculates summary statistics or other metrics for each of the identified chromatographic peaks in an xcms result object, such as the XcmsExperiment(). Different metrics can be calculated, depending upon (and configured by) using dedicated parameter classes. As a result, the method returns a matrix or data.frame with one row per chromatographic peak. Each column contains calculated values, depending on the used method/parameter class.

Currently implemented methods/parameter classes are:

• BetaDistributionParam: calculates the beta_cor and beta_snr quality metrics as described in Kumler 2023 representing the result from a (correlation) test of similarity (using Pearson's correlation coefficient) to a bell curve and the signal-to-noise ratio calculated on the residuals of this test.

Usage

chromPeakSummary(object, param, ...)

## S4 method for signature 'XcmsExperiment,BetaDistributionParam'
chromPeakSummary(
  object,
  param,
  msLevel = 1L,
  chunkSize = 2L,
  BPPARAM = bpparam()
)

BetaDistributionParam()

Arguments

object	an xcms result object containing information on identified chromatographic peaks.
param	a parameter object defining the method/summaries that should be calculated (see description above for supported parameter classes).
...	additional arguments passed to the method implementation.
msLevel	integer(1) with the MS level of the chromatographic peaks on which the metric should be calculated.
chunkSize	integer(1) defining the number of samples from which data should be loaded and processed at a time.
BPPARAM	Parallel processing setup. See BiocParallel::bpparam() for details.

Value

A matrix or data.frame with the same number of rows as there are chromatographic peaks. Columns contain the calculated values. The number of columns, their names and content depend on the used parameter object. See the respective documentation above for more details.

Author(s)

Pablo Vangeenderhuysen, Johannes Rainer, William Kumler

References

Kumler W, Hazelton B J and Ingalls A E (2023) "Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics" BMC Bioinformatics 24(1):404. doi: 10.1186/s12859-023-05533-4

sneumann/xcms documentation built on Feb. 7, 2025, 7:36 p.m.