Chromatographic peak summaries
Source:R/AllGenerics.R, R/XcmsExperiment.R, R/functions-Params.R
chromPeakSummary.RdThe 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 class '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.