groupFeaturesXCMS3: Group features using XCMS (new interface)

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Group features using XCMS (new interface)

Description

Uses the new xcms3 interface from the xcms package to find features.

Usage

groupFeaturesXCMS3(feat, ...)

## S4 method for signature 'features'
groupFeaturesXCMS3(
  feat,
  rtalign = TRUE,
  loadRawData = TRUE,
  groupParam = xcms::PeakDensityParam(sampleGroups = analysisInfo(feat)$group),
  preGroupParam = groupParam,
  retAlignParam = xcms::ObiwarpParam(),
  verbose = TRUE
)

## S4 method for signature 'featuresSet'
groupFeaturesXCMS3(
  feat,
  groupParam = xcms::PeakDensityParam(sampleGroups = analysisInfo(feat)$group),
  verbose = TRUE
)

Arguments

feat	The features object with the features to be grouped.
...	Further parameters passed to the selected grouping algorithm.
rtalign	Set to TRUE to enable retention time alignment.
loadRawData	Set to TRUE if analyses are available as mzXML or mzML files. Otherwise MS data is not loaded, and some dummy data (e.g. file paths) is used in the returned object.
groupParam, retAlignParam	parameter object that is directly passed to xcms::groupChromPeaks and xcms::adjustRtime, respectively.
preGroupParam	grouping parameters applied when features are grouped prior to alignment (only with peak groups alignment).
verbose	if FALSE then no text output will be shown.

Details

This function uses XCMS3 to group features. This function is called when calling groupFeatures with algorithm="xcms3".

Grouping of features and alignment of their retention times are performed with the xcms::groupChromPeaks and xcms::adjustRtime functions, respectively. Both of these functions support an extensive amount of parameters that modify their behavior and may therefore require optimization.

Value

An object of a class which is derived from featureGroups.

The featuresSet method (for sets workflows) returns a featureGroupsSet object.

Sets workflows

loadRawData and arguments related to retention time alignment are currently not supported for sets workflows.

References

\addCitations

xcms1

\addCitationsxcms2

\addCitationsxcms3

See Also

groupFeatures for more details and other algorithms.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.