Componentization of homologous series with nontarget

Uses the nontarget R package to generate components by unsupervised detection of homologous series.

Usage

generateComponentsNontarget(fGroups, ...)

# S4 method for class 'featureGroups'
generateComponentsNontarget(
  fGroups,
  ionization = NULL,
  rtRange = c(-120, 120),
  mzRange = c(5, 120),
  elements = c("C", "H", "O"),
  rtDev = defaultLim("retention", "wide"),
  absMzDev = defaultLim("mz", "narrow"),
  absMzDevLink = defaultLim("mz", "medium"),
  traceHack = all(R.Version()[c("major", "minor")] >= c(3, 4)),
  ...
)

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

Arguments

fGroups

featureGroups object for which components should be generated.

...

Any further arguments passed to homol.search.

(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.

rtRange

A numeric vector containing the minimum and maximum retention time (in seconds) between homologues. Series are always considered from low to high m/z, thus, a negative minimum retention time allows detection of homologous series with increasing m/z and decreasing retention times. These values set the minrt and maxrt arguments of homol.search.

mzRange

A numeric vector specifying the minimum and maximum m/z increment of a homologous series. Sets the minmz and maxmz arguments of homol.search.

elements

A character vector with elements to be considered for detection of repeating units. Sets the elements argument of homol.search function.

rtDev

Maximum retention time deviation. Sets the rttol to homol.search.

absMzDev

Maximum absolute m/z deviation. Sets the mztol argument to homol.search

absMzDevLink

Maximum absolute m/z deviation when linking series. This should usually be a bit higher than absMzDev to ensure proper linkage.

traceHack

Currently homol.search does not work with R >3.3.3. This flag, which is enabled by default on these R versions, implements a (messy) workaround (more details here).

Value

The generated comnponents are returned as an object from the componentsNT class.

Details

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

In the first step the homol.search function is used to detect all homologous series within each replicate (analyses within each replicate are averaged prior to detection). Then, homologous series across replicates are merged in case of full overlap or when merging of partial overlapping series causes no conflicts.

Sets workflows

In a sets workflow the componentization is first performed for each set independently. The resulting components are then all combined in a componentsNTSet 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").

The output class supports additional methods such as plotGraph.

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.

References

Loos M, Singer H (2017). “Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data.” Journal of Cheminformatics, 9(1). doi:10.1186/s13321-017-0197-z .

Loos M, Gerber C, Corona F, Hollender J, Singer H (2015). “Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees.” Analytical Chemistry, 87(11), 5738-5744. https://pubs.acs.org/doi/abs/10.1021/acs.analchem.5b00941.