Generate components of transformation products

Generates components by linking feature groups of transformation products and their parents.

Usage

generateComponentsTPs(fGroups, ...)

# S4 method for class 'featureGroups'
generateComponentsTPs(
  fGroups,
  fGroupsTPs = fGroups,
  TPs = NULL,
  MSPeakLists = NULL,
  formulas = NULL,
  compounds = NULL,
  ignoreParents = FALSE,
  minRTDiff = 20,
  specSimParams = getDefSpecSimParams(),
  IMS = "maybe"
)

# S4 method for class 'featureGroupsSet'
generateComponentsTPs(
  fGroups,
  fGroupsTPs = fGroups,
  TPs = NULL,
  MSPeakLists = NULL,
  formulas = NULL,
  compounds = NULL,
  ignoreParents = FALSE,
  minRTDiff = 20,
  specSimParams = getDefSpecSimParams(),
  IMS = "maybe"
)

Arguments

fGroups

The input featureGroups for componentization. See fGroupsTPs.

...

Further arguments specified to the methods.

fGroupsTPs

A featureGroups object containing the feature groups that are expected to be transformation products. If a distinction between parents and TPs is not yet known, fGroupsTPs should equal the fGroups argument. Otherwise, fGroups should only contain the parent feature groups, and both fGroups and fGroupsTPs must be a subset of the same featureGroups object.

TPs

A transformationProducts object. Set to NULL to perform linking without this data.

MSPeakLists, formulas, compounds

A MSPeakLists/formulas/compounds object to calculate MS/MS or annotation similarities between parents and TPs. If NULL then this data is not calculated. For more details see the Linking parents and transformation products section below.

ignoreParents

If TRUE then feature groups present in both fGroups and fGroupsTPs are not considered as TPs.

minRTDiff

Minimum retention time (in seconds) difference between the parent and a TP to calculate the retention order direction.

specSimParams

A named list with parameters that influence the calculation of MS spectra similarities. See the spectral similarity parameters documentation for more details.

IMS

(IMS workflow) Specifies which feature groups are considered for componentization in IMS workflows. The following options are valid:

"both": Selects IMS and non-IMS features.
"maybe": Selects non-IMS features and IMS features without assigned IMS precursor.
FALSE: Selects only non-IMS features.
TRUE: Selects only IMS features.

Value

The components are stored in objects derived from componentsTPs.

Details

This function uses transformation product screening to generate components. This function is called when calling generateComponents with algorithm="tp".

This method typically employs data from generated transformation products to find parents and their TPs. However, this data is not necessary, and components can also be made based on MS/MS similarity and/or other annotation similarities between the parent and its TPs. For more details see the Linking parents and transformation products section below.

Note

The shift parameter of specSimParams is ignored by generateComponentsTPs, since it always calculates similarities with all supported options.

Linking parents and transformation products

Each component consists of feature groups that are considered to be transformation products for one parent (the parent that 'belongs' to the component can be retrieved with the componentInfo method). The parent feature groups are taken from the fGroups parameter, while the feature groups for TPs are taken from fGroupsTPs. If a feature group occurs in both variables, it may therefore be considered as both a parent or TP.

If transformation product data is given, i.e. the TPs argument is set, then a suspect screening of the parents and/or TPs may need to be performed in advance to facilitate linkage. This depends on the algorithm that was used to generate the TPs:

the parents need to be screened for all algorithms except logic (generateTPsLogic)
the TPs need to be screened for all algorithms except ann_form and ann_comp (generateTPsAnnForm and generateTPsAnnComp).

See screenSuspects to perform the screening and convertToSuspects to create the suspect list. To include parents make sure to set includeParents=TRUE when calling convertToSuspects or first screen for the parents and then amend the screening object with TP screening results by setting amend=TRUE to screenSuspects. If the the suspect screening yields multiple TP hits, all will be reported. Similarly, if the suspect screening contains multiple hits for a parent, a component is made for each of the parent hits.

In case no transformation product data is provided (TPs=NULL), the componentization algorithm simply assumes that each feature group from fGroupsTPs is a potential TP for every parent feature group in fGroups. For this reason, it is highly recommended to specify which feature groups are parents/TPs (see the fGroupsTPs argument description above) and crucial that the data is post-processed, for instance by only retaining TPs that have high annotation similarity with their parents (see the filter method for componentsTPs).

A typical way to distinguish which feature groups are parents or TPs from two different (groups of) samples is by calculating Fold Changes (see the as.data.table method for feature groups and plotVolcano). Of course, other statistical techniques from R are also suitable.

Result columns

During componentization, several characteristics are calculated which may be useful for post-processing. These can be obtained with e.g. as.data.table or componentTable. The properties are either reported for each feature group in a component, or for each candidate of a feature group in a component (only if TPs was set).

The following properties may be reported for each feature group:

specSimilarity: the MS/MS spectral similarity between the feature groups of the TP and its parent (0-1).
specSimilarityPrec,specSimilarityBoth: as specSimilarity, but calculated with binned data using the "precursor" and "both" method, respectively (see MS spectral similarity parameters for more details).
totalFragmentMatches The total number of MS/MS fragment annotations that overlap between all feature annotation candidates for the TP feature group and the feature annotations specifically for the parent (based on the assigned fragment formula). If both the formulas and compounds arguments are specified then the annotation data is pooled prior to calculation. Each unique match is only counted once.
totalNeutralLossMatches As totalFragmentMatches, but counting overlapping neutral loss formulae.
retDir,TP_retDir The retention order direction derived from the feature groups (retDir) or the (expected) value from TP data (TP_retDir).
retDiff,mzDiff, The retention time and m/z difference between the parent and TP.

The candidate specific properties are stored inside the candidates column in component tables, and can be obtained with as.data.table by setting candidates=TRUE. The following properties may be present:

fragmentMatches,neutralLossMatches As totalFragmentMatches and totalNeutralLossMatches, but only considering the feature annotations specifically for this candidate.
formulaDiff The formula difference between the parent and TP (if formula data is available).
TPScore,annSim,fitFormula,fitCompound,simSusps: TP scoring properties, see generateTPsAnnForm and generateTPsAnnComp.

IMS workflows

In IMS workflows with post mobility assignment (see assignMobilities) it may be necessary to call expandForIMS when componentization was performed prior to mobility assignments, see its documentation for more details.

If mobilities were already assigned prior to componentization, then the IMS argument selects which feature groups are subjected to componentization. Data for IMS feature groups that were not considered (i.e. when IMS is FALSE or "maybe"), will be expanded similarly as is done by expandForIMS.

NOTE: IMS expansion by expandForIMS only expands results for TP candidates, i.e. no new components from parents assigned to IMS feature groups will be added.

Sets workflows

In a sets workflow the component tables are amended with extra information such as overall/specific set spectrum similarities. As sets data is mixed, transformation products are able to be linked with a parent, even if they were not measured in the same set.