groupFeaturesXCMS: Group features using XCMS (old interface)

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

Group features using XCMS (old interface)

Description

Group and align features with the legacy xcmsSet function from the xcms package.

Usage

groupFeaturesXCMS(feat, ...)

## S4 method for signature 'features'
groupFeaturesXCMS(
  feat,
  rtalign = TRUE,
  loadRawData = TRUE,
  groupArgs = list(mzwid = 0.015),
  retcorArgs = list(method = "obiwarp"),
  verbose = TRUE
)

## S4 method for signature 'featuresSet'
groupFeaturesXCMS(feat, groupArgs = list(mzwid = 0.015), 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.
groupArgs	named character vector that may contain extra grouping parameters to be used by xcms::group
retcorArgs	named character vector that may contain extra parameters to be used by xcms::retcor.
verbose	if FALSE then no text output will be shown.

Details

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

Grouping of features and alignment of their retention times are performed with the xcms::group and xcms::retcor functions, respectively. Both functions have an extensive list of parameters to modify their behavior and may therefore be used to potentially optimize results.

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.