groupFeaturesKPIC2: Group features using KPIC2

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

Group features using KPIC2

Description

Uses the the KPIC2 R package for grouping of features.

Usage

groupFeaturesKPIC2(feat, ...)

## S4 method for signature 'features'
groupFeaturesKPIC2(
  feat,
  rtalign = TRUE,
  loadRawData = TRUE,
  groupArgs = list(tolerance = c(0.005, 12)),
  alignArgs = list(),
  verbose = TRUE
)

## S4 method for signature 'featuresSet'
groupFeaturesKPIC2(
  feat,
  groupArgs = list(tolerance = c(0.005, 12)),
  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, alignArgs	Named character vector that may contain extra parameters to be used by KPIC::PICset.group and KPIC::PICset.align, respectively.
verbose	if FALSE then no text output will be shown.

Details

This function uses KPIC2 to group features. This function is called when calling groupFeatures with algorithm="kpic2".

Grouping of features and alignment of their retention times are performed with the KPIC::PICset.group and KPIC::PICset.align functions, respectively.

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

\insertRef

Ji2017patRoon

See Also

groupFeatures for more details and other algorithms.

rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.