components-class: Component class

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Component class

Description

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)

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

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

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

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

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

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

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

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

## S4 method for signature 'components'
x$name

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

obj, object, x	The component object.
fGroup	The name (thus a character) of the feature group that should be searched for.
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).
...	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 colourBy, 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. \setsPassedArgs 1components
drop	ignored.
name	The component name (partially matched).
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.
fGroups	The featureGroups object that was used to generate the components.
EICParams	A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation for more details.
sets	\setsWF A character with name(s) of the sets to keep (or remove if negate=TRUE).
set	\setsWF The name of the set.

Details

components objects are obtained from generateComponents.

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.

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.

• 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.

S4 class hierarchy

• workflowStep

  • components

    • componentsCamera

    • componentsFeatures

      • componentsCliqueMS

      • componentsOpenMS

    • componentsClust

      • componentsIntClust

      • componentsSpecClust

    • componentsSet

      • componentsNTSet

    • componentsUnset

    • componentsNT

      • componentsNTUnset

    • componentsRC

    • componentsTPs

Sets workflows

\setsWFClass

componentsSetcomponents

\setsWFNewMethodsSO

componentsUnsetOnly the components in the specified set are kept.

\setsWFChangedMethods \item

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

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 topMostByRGroup EIC parameters are ignored unless the components are from homologous series.

See Also

generateComponents

rickhelmus/patRoon documentation built on April 3, 2024, 6:56 p.m.