Componentization of adducts, isotopes etc. with RAMClustR

Uses RAMClustR to generate components from feature groups which follow similar chromatographic retention profiles and annotate their relationships (e.g. adducts and isotopes).

Usage

generateComponentsRAMClustR(fGroups, ...)

# S4 method for class 'featureGroups'
generateComponentsRAMClustR(
  fGroups,
  ionization = NULL,
  st = NULL,
  sr = NULL,
  maxt = 12,
  hmax = 0.3,
  normalize = "TIC",
  absMzDev = defaultLim("mz", "narrow"),
  relMzDev = defaultLim("mz", "narrow_rel"),
  minSize = 2,
  relMinReplicates = 0.5,
  RCExperimentVals = list(design = list(platform = "LC-MS"), instrument = list(ionization
    = ionization, MSlevs = 1)),
  extraOptsRC = NULL,
  extraOptsFM = NULL
)

# S4 method for class 'featureGroupsSet'
generateComponentsRAMClustR(fGroups, ionization = NULL, ...)

Arguments

fGroups

featureGroups object for which components should be generated.

...

(sets workflow) Further arguments passed to the non-sets workflow method.

ionization

Which ionization polarity was used to generate the data: should be "positive" or "negative". If the featureGroups object has adduct annotations, and ionization=NULL, the ionization will be detected automatically.

(sets workflow) This parameter is not supported for sets workflows, as the ionization will always be detected automatically.

st, sr, maxt, hmax, normalize

Arguments to tune the behaviour of feature group clustering. See their documentation from ramclustR. When st is NULL it will be automatically calculated as the half of the median for all chromatographic peak widths.

absMzDev

Maximum absolute m/z deviation. Sets the mzabs.error argument to do.findmain

relMzDev

Maximum relative mass deviation (ppm). Sets the ppm.error argument to do.findmain.

minSize

The minimum size of a component. Smaller components than this size will be removed. See note below. Sets the minModuleSize argument to ramclustR.

relMinReplicates

Feature groups within a component are only kept when they contain data for at least this (relative) amount of replicate analyses. For instance, 0.5 means that at least half of the replicates should contain data for a particular feature group in a component. In this calculation replicates that are fully absent within a component are not taken in to account. See note below.

RCExperimentVals

A named list containing two more lists: design and instrument. These are used to construct the ExpDes argument passed to ramclustR.

extraOptsRC, extraOptsFM

Named list with further arguments to be passed to ramclustR and do.findmain. Set to NULL to ignore.

Value

A components (derived) object containing all generated components.

Details

This function uses RAMClustR to generate components. This function is called when calling generateComponents with algorithm="ramclustr".

This method uses the ramclustR functions for generating the components, whereas do.findmain is used for annotation.

Note

The default value for relMinReplicates results in extra filtering, hence, the final results may be different than what the algorithm normally would return.

IMS workflows

The componentization algorithm is not aware of the IMS dimension. For this reason, no IMS feature groups will be considered for componentization, and direct IMS workflows (see assignMobilitities) are currently not supported.

Sets workflows

In a sets workflow the componentization is first performed for each set independently. The resulting components are then all combined in a componentsSet object. Note that the components themselves are never merged. The components are renamed to include the set name from which they were generated (e.g. "CMP1" becomes "CMP1-positive").

References

Broeckling, Heuberger CD;, Prince AL;, Ingelsson JA;, Prenni E;, E. J (2013). “Assigning precursor-product ion relationships in indiscriminant MS/MS data from non-targeted metabolite profiling studies.” Analytical Chemistry, 9, 33-43.

Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE (2014). “RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data.” Analytical Chemistry, 86 (14), 6812–6817.