generateComponentsRAMClustR: Componentization of adducts, isotopes etc. with RAMClustR

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

Componentization of adducts, isotopes etc. with RAMClustR

Description

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 signature 'featureGroups'
generateComponentsRAMClustR(
  fGroups,
  ionization = NULL,
  st = NULL,
  sr = NULL,
  maxt = 12,
  hmax = 0.3,
  normalize = "TIC",
  absMzDev = 0.002,
  relMzDev = 5,
  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 signature 'featureGroupsSet'
generateComponentsRAMClustR(fGroups, ionization = NULL, ...)

Arguments

fGroups	featureGroups object for which components should be generated.
...	\setsWF 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. \setsWF 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.

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.

Value

A components (derived) object containing all generated components.

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").

Note

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

References

\insertRef

Broeckling2013patRoon

\insertRefBroeckling2014patRoon

See Also

generateComponents for more details and other algorithms.

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