Group features using KPIC2

Uses the the KPIC2 R package for grouping of features.

Usage

groupFeaturesKPIC2(feat, ...)

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

# S4 method for class '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.

Value

An object of a class which is derived from featureGroups.

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.

Sets workflows

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

References

Ji H, Zeng F, Xu Y, Lu H, Zhang Z (2017). “KPIC2: An Effective Framework for Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms.” Analytical Chemistry, 89(14), 7631–7640. doi:10.1021/acs.analchem.7b01547 .