R/TP-structure.R, R/TP-CTS.R, R/TP-biotransformer.R, and 1 more
transformationProductsStructure-class.RdHolds information for all TPs for a set of parents, including structural information.
# 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 = length(list(...)) + 1,
nintersects = NA,
upsetArgs = NULL
)
# S4 method for class 'transformationProductsStructure'
consensus(
obj,
...,
absMinAbundance = NULL,
relMinAbundance = NULL,
uniqueFrom = NULL,
uniqueOuter = FALSE,
labels = NULL
)The file name of the the output MetFrag database.
Set to TRUE to include the parents in the database.
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.
If TRUE then TPs with an equal formula as their parent (isomers) are removed.
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.
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.
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).
If set to FALSE then no text output is shown.
If TRUE then filters are performed in opposite manner.
Either a character or integer vector with one or more names/indices of the parents to
plot.
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.
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.
If TRUE and components is set, then pathways without any detected TPs are not shown
(pruned). See also the onlyCompletePaths and components arguments.
If TRUE and components is set, then only pathways are shown for which
all TPs were detected. See also the prune and components arguments.
Passed to visNetwork.
Only consider TPs from parents that are common to all compared objects.
A character with names to use for labelling. If NULL labels are automatically generated.
A list with further arguments passed to VennDiagram plotting functions. Set to
NULL to ignore.
See upset.
A list with any further arguments to be passed to
upset. Set to NULL to ignore.
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.
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.
If uniqueFrom is not NULL and if
uniqueOuter=TRUE: only retain data that are also unique between
objects specified in uniqueFrom.
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.
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.
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.
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.
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.
transformationProductsStructure
transformationProductsStructureConsensus
transformationProductsCTS
transformationProductsBT
transformationProductsLibrary
Conway2017patRoon
Lex2014patRoon
The base class transformationProducts for more relevant methods and generateTPs