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Comparing feature groups

Source: R/generics.R, R/feature_groups-comparison.R
featureGroups-compare.Rd

Functionality to compare feature groups and make a consensus.

Usage

comparison(..., groupAlgo, groupArgs = list(rtalign = FALSE))

# S4 method for class 'featureGroups'
comparison(..., groupAlgo, groupArgs = list(rtalign = FALSE))

# S4 method for class 'featureGroupsComparison'
hasIMS(obj)

# S4 method for class 'featureGroupsComparison,missing'
plot(x, retMin = FALSE, ...)

# S4 method for class 'featureGroupsComparison'
plotVenn(obj, which = NULL, ...)

# S4 method for class 'featureGroupsComparison'
plotUpSet(obj, which = NULL, ...)

# S4 method for class 'featureGroupsComparison'
plotChord(obj, addSelfLinks = FALSE, addRetMzPlots = TRUE, ...)

# S4 method for class 'featureGroupsComparison'
consensus(
  obj,
  absMinAbundance = NULL,
  relMinAbundance = NULL,
  uniqueFrom = NULL,
  uniqueOuter = FALSE,
  verifyAnaInfo = TRUE
)

# S4 method for class 'featureGroupsSet'
comparison(..., groupAlgo, groupArgs = list(rtalign = FALSE))

# S4 method for class 'featureGroupsComparisonSet'
consensus(obj, ...)

Arguments

...

For comparison: featureGroups objects that should be compared. If the arguments are named (e.g. myGroups = fGroups) then these are used for labelling, otherwise objects are automatically labelled by their algorithm.

For plot, plotVenn, plotChord: further options passed to plot, VennDiagram plotting functions (e.g. draw.pairwise.venn) and chordDiagram respectively.

For plotUpSet: any further arguments passed to the plotUpSet method defined for featureGroups.

groupAlgo

The feature grouping algorithm that should be used for grouping pseudo features (see details). Valid values are: "xcms", xcms3, kpic2, "openms" or "greedy".

(IMS workflow) For IMS workflows the algorithm selection is equally limited to as what is used by feature grouping, i.e. only greedy is currently supported.

groupArgs

A list containing further parameters for feature grouping.

x, obj

The featureGroupsComparison object.

retMin

If TRUE retention times are plotted as minutes (seconds otherwise).

which

A character vector specifying one or more labels of compared feature groups. For plotVenn: if NULL then all compared groups are used.

If TRUE then 'self-links' are added which represent non-shared data.

addRetMzPlots

Set to TRUE to enable m/z vs retention time scatter plots.

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 feature groups 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.

verifyAnaInfo

If FALSE then the analysis information is not verified to be equal for all compared objects. This is mainly only useful when the data is the same but stored in different formats (e.g. mzXML/mzML).

Value

comparison returns a featureGroupsComparison object.

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 featureGroups object with a consensus from the compared feature groups.

Details

Feature groups objects originating from differing feature finding and/or grouping algorithms (or their parameters) may be compared to assess their output and generate a consensus.

The comparison method generates a featureGroupsComparison object from given feature groups objects, which in turn may be used for (visually) comparing presence of feature groups and generating a consensus. Internally, this function will collapse each feature groups object to pseudo features objects by averaging their retention times, m/z values and intensities, where each original feature groups object becomes an 'analysis'. All pseudo features are then grouped using regular feature grouping algorithms so that a comparison can be made.

hasIMS returns TRUE if the object has ion mobility information.

plot generates an m/z vs retention time plot.

plotVenn plots a Venn diagram outlining unique and shared feature groups between up to five compared feature groups.

plotUpSet plots an UpSet diagram outlining unique and shared feature groups.

plotChord plots a chord diagram to visualize the distribution of feature groups.

consensus combines all compared feature groups and averages their retention, m/z and intensity data. Not yet supported for sets workflows.