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Base transformation products (TP) class with structure information

Source: R/TP-structure.R, R/TP-CTS.R, R/TP-biotransformer.R, and 1 more
transformationProductsStructure-class.Rd

Holds information for all TPs for a set of parents, including structural information.

Usage

# S4 method for class 'transformationProductsStructure'
convertToMFDB(TPs, out, includeParents = FALSE)

# S4 method for class 'transformationProductsStructure'
filter(
  obj,
  ...,
  removeParentIsomers = FALSE,
  removeTPIsomers = FALSE,
  removeDuplicates = FALSE,
  minSimilarity = NULL,
  verbose = TRUE,
  negate = FALSE
)

# S4 method for class 'transformationProductsStructure'
plotGraph(
  obj,
  which,
  components = NULL,
  structuresMax = 25,
  prune = TRUE,
  onlyCompletePaths = FALSE,
  width = NULL,
  height = NULL
)

# S4 method for class 'transformationProductsStructure'
plotVenn(obj, ..., commonParents = FALSE, labels = NULL, vennArgs = NULL)

# S4 method for class 'transformationProductsStructure'
plotUpSet(
  obj,
  ...,
  commonParents = FALSE,
  labels = NULL,
  nsets = NULL,
  nintersects = NA,
  upsetArgs = NULL
)

# S4 method for class 'transformationProductsStructure'
consensus(
  obj,
  ...,
  absMinAbundance = NULL,
  relMinAbundance = NULL,
  uniqueFrom = NULL,
  uniqueOuter = FALSE,
  labels = NULL
)

Arguments

out

The file name of the the output MetFrag database.

includeParents

Set to TRUE to include the parents in the database.

obj, TPs

transformationProductsStructure derived object to be accessed

...

For filter: Further argument passed to the base filter method.

For plotVenn, plotUpSet and consensus: further (unique) transformationProductsStructure objects.

removeParentIsomers

If TRUE then TPs with an equal formula as their parent (isomers) are removed.

removeTPIsomers

If TRUE then all TPs with equal formula as any sibling TPs (isomers) are removed. Unlike removeDuplicates, all TP candidates are removed (including the first match). This filter automatically sets removeDuplicates=TRUE so that TPs are only removed if with different structure.

removeDuplicates

If TRUE then the TPs of a parent with duplicate structures (SMILES) are removed. Such duplicates may occur when different transformation pathways yield the same TPs. The first TP candidate with duplicate structure will be kept.

minSimilarity

Minimum structure similarity (0-1) that a TP should have relative to its parent. This data is only available if the calcSims argument to generateTPs was set to TRUE. May be useful under the assumption that parents and TPs who have a high structural similarity, also likely have a high MS/MS spectral similarity (which can be evaluated after componentization with generateComponentsTPs. Any values that are NA are removed (which only occur when a consensus was made from objects that not all have similarity information).

verbose

If set to FALSE then no text output is shown.

negate

If TRUE then filters are performed in opposite manner.

which

Either a character or integer vector with one or more names/indices of the parents to plot.

components

If specified (i.e. not NULL), a componentsTPs object that is used for matching the graph with screening results. The TPs that were found will be marked. See also the prune and onlyCompletePaths arguments.

structuresMax

An integer with the maximum number of structures to plot. Setting a maximum is mainly done to avoid long times needed to construct the graph.

prune

If TRUE and components is set, then pathways without any detected TPs are not shown (pruned). See also the onlyCompletePaths and components arguments.

onlyCompletePaths

If TRUE and components is set, then only pathways are shown for which all TPs were detected. See also the prune and components arguments.

width, height

Passed to visNetwork.

commonParents

Only consider TPs from parents that are common to all compared objects.

labels

A character with names to use for labelling. If NULL labels are automatically generated.

vennArgs

A list with further arguments passed to VennDiagram plotting functions. Set to NULL to ignore.

nsets, nintersects

See upset. If nsets == NULL then it will be set to the number of compared items.

upsetArgs

A list with any further arguments to be passed to upset. Set to NULL to ignore.

absMinAbundance, relMinAbundance

Minimum absolute or relative (0-1) abundance across objects for a result to be kept. For instance, relMinAbundance=0.5 means that a result should be present in at least half of the number of compared objects. Set to NULL to ignore and keep all results. Limits cannot be set when uniqueFrom is not NULL.

uniqueFrom

Set this argument to only retain TPs that are unique within one or more of the objects for which the consensus is made. Selection is done by setting the value of uniqueFrom to a logical (values are recycled), numeric (select by index) or a character (as obtained with algorithm(obj)). For logical and numeric values the order corresponds to the order of the objects given for the consensus. Set to NULL to ignore.

uniqueOuter

If uniqueFrom is not NULL and if uniqueOuter=TRUE: only retain data that are also unique between objects specified in uniqueFrom.

Value

filter returns a filtered transformationProductsStructure object.

plotGraph returns the result of visNetwork.

plotVenn (invisibly) returns a list with the following fields:

  • gList the gList object that was returned by the utilized VennDiagram plotting function.

  • areas The total area for each plotted group.

  • intersectionCounts The number of intersections between groups.

The order for the areas and intersectionCounts fields is the same as the parameter order from the used plotting function (see e.g. draw.pairwise.venn and draw.triple.venn).

consensus returns a transformationProductsStructure object that is produced by merging results from multiple transformationProductsStructure objects.

Details

This (virtual) class is derived from the transformationProducts base class, please see its documentation for more details. Objects from this class are returned by TP generators. More specifically, algorithms that works with chemical structures (e.g. biotransformer), uses this class to store their results. The methods defined for this class extend the functionality for the base transformationProducts class.

Methods (by generic)

  • convertToMFDB(transformationProductsStructure): Exports this object as a .csv file that can be used as a MetFrag local database. Any duplicate TPs (formed by different pathways or parents) will be merged based on their InChIKey.

  • filter(transformationProductsStructure): Performs rule-based filtering. Useful to simplify and clean-up the data.

  • plotGraph(transformationProductsStructure): Plots an interactive hierarchy graph of the transformation products. The resulting graph can be browsed interactively and allows exploration of the different TP formation pathways. Furthermore, results from TP componentization can be used to match the hierarchy with screening results. The graph is rendered with visNetwork.

  • plotVenn(transformationProductsStructure): plots a Venn diagram (using VennDiagram) outlining unique and shared candidates of up to five different featureAnnotations objects.

  • plotUpSet(transformationProductsStructure): Plots an UpSet diagram (using the upset function) outlining unique and shared TPs between different transformationProductsStructure objects.

  • consensus(transformationProductsStructure): Generates a consensus from different transformationProductsStructure objects. Currently this removes any hierarchical data, and all TPs are considered to originate from the same (original) parent.

Note

consensus: If the retDir values differs between matched TPs it will be set to 0. If structure similarity data is available (i.e. calcSims=TRUE to generateTPs) then the mean similarity is calculated.

Comparison between objects

The methods that compare different objects (e.g. plotVenn and consensus) use the InChIKey to match TPs between objects. Moreover, the parents between objects are matched by their name. Hence, it is crucial that the input parents to generateTPs (i.e. the parents argument) are named equally.

S4 class hierarchy

References

Conway JR, Lex A, Gehlenborg N (2017). “UpSetR: an R package for the visualization of intersecting sets and their properties.” Bioinformatics, 33(18), 2938-2940. doi:10.1093/bioinformatics/btx364 . http://dx.doi.org/10.1093/bioinformatics/btx364.

Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H (2014). “UpSet: Visualization of Intersecting Sets.” IEEE Transactions on Visualization and Computer Graphics, 20(12), 1983–1992. doi:10.1109/tvcg.2014.2346248 .

See also

The base class transformationProducts for more relevant methods and generateTPs