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Component class

Source: R/generics.R, R/components.R, R/components-camera.R, and 9 more
components-class.Rd

Contains data for feature groups that are related in some way. These components commonly include adducts, isotopes and homologues.

Usage

componentTable(obj)

componentInfo(obj)

findFGroup(obj, fGroup)

expandForIMS(obj, ...)

# S4 method for class 'components'
componentTable(obj)

# S4 method for class 'components'
componentInfo(obj)

# S4 method for class 'components'
groupNames(obj)

# S4 method for class 'components'
length(x)

# S4 method for class 'components'
names(x)

# S4 method for class 'components'
show(object)

# S4 method for class 'components,ANY,ANY,missing'
x[i, j, ..., drop = TRUE]

# S4 method for class 'components,ANY,ANY'
x[[i, j]]

# S4 method for class 'components'
x$name

# S4 method for class 'components'
delete(obj, i = NULL, j = NULL, ...)

# S4 method for class 'components'
as.data.table(x)

# S4 method for class 'components'
expandForIMS(obj, fGroups)

# S4 method for class 'components'
filter(
  obj,
  size = NULL,
  adducts = NULL,
  isotopes = NULL,
  rtIncrement = NULL,
  mzIncrement = NULL,
  checkComponentsSession = NULL,
  negate = FALSE,
  verbose = TRUE
)

# S4 method for class 'components'
findFGroup(obj, fGroup)

# S4 method for class 'components'
plotSpectrum(obj, index, markFGroup = NULL, xlim = NULL, ylim = NULL, ...)

# S4 method for class 'components'
plotChroms(obj, index, fGroups, EICParams = getDefEICParams(window = 5), ...)

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

# S4 method for class 'componentsCamera'
expandForIMS(obj, ...)

# S4 method for class 'componentsFeatures'
show(object)

# S4 method for class 'componentsCliqueMS'
expandForIMS(obj, ...)

# S4 method for class 'componentsSet'
show(object)

# S4 method for class 'componentsSet,ANY,ANY,missing'
x[i, j, ..., sets = NULL, drop = TRUE]

# S4 method for class 'componentsSet'
filter(obj, ..., negate = FALSE, sets = NULL)

# S4 method for class 'componentsSet'
delete(obj, i = NULL, j = NULL, ...)

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

# S4 method for class 'componentsSet'
expandForIMS(obj, fGroups)

# S4 method for class 'componentsSet'
unset(obj, set)

# S4 method for class 'componentsNet'
expandForIMS(obj, ...)

# S4 method for class 'componentsNetSet'
expandForIMS(obj, ...)

# S4 method for class 'componentsNT'
expandForIMS(obj, ...)

# S4 method for class 'componentsNTSet'
expandForIMS(obj, ...)

# S4 method for class 'componentsOpenMS'
expandForIMS(obj, ...)

# S4 method for class 'componentsRC'
expandForIMS(obj, ...)

Arguments

obj, object, x

The component object.

fGroup

The name (thus a character) of the feature group that should be searched for.

...

For delete: passed to the function specified as j.

For plotChroms: Further (optional) arguments passed to the plotChroms method for the featureGroups class. Note that the groupBy, showPeakArea, showFGroupRect and topMost arguments cannot be set as these are set by this method.

For plotSpectrum: Further arguments passed to plot.

For consensus: components objects that should be used to generate the consensus.

For sets workflow methods: further arguments passed to the base components method.

i, j

For [/[[: A numeric or character value which is used to select components/feature groups by their index or name, respectively (for the order/names see names()/groupNames()).

For [: Can also be logical to perform logical selection (similar to regular vectors). If missing all components/feature groups are selected.

For [[: should be a scalar value. j is optional.

For delete: The data to remove from. i are the components as numeric index, logical or character, j the feature groups as numeric index/logical (relative to component) or character. If either is NULL then data for all is removed. j may also be a function: it will be called for each component, with the component (a data.table), the component name and any other arguments passed as ... to delete. The return value of this function specifies the feature groups to be removed (same format as j).

drop

ignored.

name

The component name (partially matched).

fGroups

The featureGroups object that was used to generate the components.

For expandForIMS, this should be the featureGroups object that contains the post IMS feature groups.

size

Should be a two sized vector with the minimum/maximum size of a component. Set to NULL to ignore.

adducts

Remove any feature groups within components that do not match given adduct rules. If adducts is a logical then only results are kept when an adduct is assigned (adducts=TRUE) or not assigned (adducts=FALSE). Otherwise, if adducts contains one or more adduct objects (or something that can be converted to it with as.adduct) then only results are kept that match the given adducts. Set to NULL to ignore this filter.

isotopes

Only keep results that match a given isotope rule. If isotopes is a logical then only results are kept with (isotopes=TRUE) or without (isotopes=FALSE) isotope assignment. Otherwise isotopes should be a numeric vector with isotope identifiers to keep (e.g. 0 for monoisotopic results, 1 for M+1 results etc.). Set to NULL to ignore this filter.

rtIncrement, mzIncrement

Should be a two sized vector with the minimum/maximum retention or mz increment of a homologous series. Set to NULL to ignore.

checkComponentsSession

If set then components and/or feature groups are removed that were selected for removal (see check-GUI and the checkComponents function). The value of checkComponentsSession should either by a path to the session file or TRUE, in which case the default session file name is used. If negate=TRUE then all non-selected data is removed instead.

negate

If TRUE then filters are applied in opposite manner.

verbose

If set to FALSE then no text output is shown.

index

The index of the component. Can be a numeric index or a character with its name.

markFGroup

If specified (i.e. not NULL) this argument can be used to mark a feature group in the plotted spectrum. The value should be a character with the name of the feature group. Setting this to NULL will not mark any peak.

xlim, ylim

Sets the plot size limits used by plot. Set to NULL for automatic plot sizing.

EICParams

A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation for more details.

sets

(sets workflow) A character with name(s) of the sets to keep (or remove if negate=TRUE).

set

(sets workflow) The name of the set.

Value

delete returns the object for which the specified data was removed.

consensus returns a components object that is produced by merging multiple specified components objects.

Details

components objects are obtained from generateComponents.

Methods (by generic)

  • componentTable(components): Accessor method for the components slot of a components class. Each component is stored as a data.table.

  • componentInfo(components): Accessor method for the componentInfo slot of a components class.

  • groupNames(components): returns a character vector with the names of the feature groups for which data is present in this object.

  • length(components): Obtain total number of components.

  • names(components): Obtain the names of all components.

  • show(components): Show summary information for this object.

  • x[i: Subset on components/feature groups.

  • x[[i: Extracts a component table, optionally filtered by a feature group.

  • $: Extracts a component table by component name.

  • delete(components): Completely deletes specified (parts of) components.

  • as.data.table(components): Returns all component data in a table.

  • expandForIMS(components): Expands the components data for IMS feature groups. See the IMS expansion section below.

  • filter(components): Provides rule based filtering for components.

  • findFGroup(components): Returns the component id(s) to which a feature group belongs.

  • plotSpectrum(components): Plot a pseudo mass spectrum for a single component.

  • plotChroms(components): Plot an extracted ion chromatogram (EIC) for all feature groups within a single component.

  • consensus(components): Generates a consensus from multiple components objects. At this point results are simply combined and no attempt is made to merge similar components.

Slots

components

List of all components in this object. Use the componentTable method for access.

componentInfo

A data.table containing general information for each component. Use the componentInfo method for access.

Note

filter Applies only those filters for which a component has data available. For instance, filtering by adduct will only filter any results within a component if that component contains adduct information.

For plotChroms: The topMost and topMostByReplicate EIC parameters are ignored unless the components are from homologous series.

S4 class hierarchy

IMS expansion

In IMS workflows with post mobility assignment (see assignMobilities), specifically when the assignment occurs after generation of the components, it may be desired to copy the results of the IMS precursors to the IMS feature groups. For instance, for components from intensity clusters or TPs one could assume that results for IMS feature groups will be largely the same as their IMS precursors. The expandForIMS method function is used to expand the original components object by adding in IMS feature groups with data copied from their IMS precursors.

Currently, only components generated with generateComponentsIntClust, generateComponentsSpecClust and generateComponentsTPs support this operation.

Sets workflows

The componentsSet class is applicable for sets workflows. This class is derived from components and therefore largely follows the same user interface.

The following methods are specifically defined for sets workflows:

  • unset Converts the object data for a specified set into a 'non-set' object (componentsUnset), which allows it to be used in 'regular' workflows. Only the components in the specified set are kept.

The following methods are changed or with new functionality:

  • filter and the subset operator ([) Can be used to select components that are only present for selected sets.

See also

generateComponents