AbstractTopDownSet-class: The AbstractTopDownSet class

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

The AbstractTopDownSet class

Description

Abstract/VIRTUAL parent class for TopDownSet and NCBSet to provide common interface.

Usage

## S4 method for signature 'AbstractTopDownSet,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'AbstractTopDownSet,ANY,missing'
x[[i, j, ...]]

## S4 replacement method for signature 'AbstractTopDownSet,ANY,missing'
x[[i, j, ...]] <- value

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

## S4 replacement method for signature 'AbstractTopDownSet'
x$name <- value

## S4 method for signature 'AbstractTopDownSet'
assayData(object)

## S4 method for signature 'AbstractTopDownSet'
colData(object)

## S4 replacement method for signature 'AbstractTopDownSet'
colData(object, ...) <- value

## S4 method for signature 'AbstractTopDownSet,AbstractTopDownSet'
combine(x, y)

## S4 method for signature 'AbstractTopDownSet'
conditionData(object, ...)

## S4 replacement method for signature 'AbstractTopDownSet'
conditionData(object, ...) <- value

## S4 method for signature 'AbstractTopDownSet'
conditionNames(object)

## S4 method for signature 'AbstractTopDownSet'
dim(x)

## S4 method for signature 'AbstractTopDownSet'
dimnames(x)

## S4 method for signature 'AbstractTopDownSet'
removeEmptyConditions(object)

## S4 method for signature 'AbstractTopDownSet'
rowViews(object, ...)

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

## S4 method for signature 'AbstractTopDownSet'
summary(object, what = c("rows", "columns"), ...)

## S4 method for signature 'AbstractTopDownSet'
updateConditionNames(
  object,
  sampleColumns = c("Mz", "AgcTarget", "EtdReagentTarget", "EtdActivation",
    "CidActivation", "HcdActivation", "UvpdActivation"),
  verbose = interactive()
)

## S4 method for signature 'AbstractTopDownSet'
updateMedianInjectionTime(
  object,
  by = list(Mz = object$Mz, AgcTarget = object$AgcTarget)
)

Arguments

i, j	numeric, logical or character, indices specifying elements to extract or replace.
drop	logical, currently ignored.
value	replacment value.
name	character name of an (non)existing column in colData.
object, x	AbstractTopDownSet
y	AbstractTopDownSet
what	character, specifies whether "rows" or "columns" should be summarized.
sampleColumns	character, column names of the colData() used to define a sample (technical replicate). This is used to add the Sample column (used for easier aggregation, etc.).
verbose	logical, verbose output?
by	list, grouping information.
...	arguments passed to internal/other methods.

Details

This class just provides a common interface. It is not intended for direct use by the user. Please see TopDownSet for an example usage of its child class.

Value

This is an Abstract/VIRTUAL class to provide a common interface for TopDownSet and NCBSet. It is not possible to create an AbstractTopDownSet object.

Methods (by generic)

• x[i: Subset operator.

  For i numeric, logical or character vectors or empty (missing) or NULL are supported. Subsetting is done on the fragment/bond (row) level. character indices could be names (e.g. c("a1", "b1", "c1", "c2", "c3")) or types (e.g. c("c", "x")) of the fragments for TopDownSet objects, or names of the bonds (e.g. c("bond001")) for NCBSet objects.
  j could be a numeric or logical vector and subsetting is done on the condition/run (column) level.

• x[[i: Subset operator.

  i could be a numeric or logical vector and subsetting is done on the condition/run (column) level.

• `[[`(x = AbstractTopDownSet, i = ANY, j = missing) <- value: Setter for a column in the colData slot.

  The ⁠[[<-⁠ operator is used to add/replace a single column of the colData DataFrame.

• $: Accessor for columns in the colData slot.

  The $ simplifies the accession of a single column of the colData. It is identical to the [[ operator.

• `$`(AbstractTopDownSet) <- value: Setter for a column in the colData slot.

  The ⁠$<-⁠ operator is used to add/replace a single column of the colData DataFrame. It is identical to the ⁠[[<-⁠ operator.

• assayData(AbstractTopDownSet): Accessor for the assay slot.

  Returns a Matrix::dgCMatrix that stores the intensity/coverage information of AbstractTopDownSet object.

• colData(AbstractTopDownSet): Accessor for the colData slot.

  Returns a S4Vectors::DataFrame that stores metadata for the conditons/runs (columns) of the AbstractTopDownSet object.

• colData(AbstractTopDownSet) <- value: Setter for the colData slot.

  Replaces metadata for the conditons/runs (columns) of the AbstractTopDownSet object.

• combine(x = AbstractTopDownSet, y = AbstractTopDownSet): Combine AbstractTopDownSet objects.

  combine allows to combine two or more AbstractTopDownSet objects. Please note that it uses the default sampleColumns to define technical replicates (see readTopDownFiles()).and the default by argument to group ion injection times for the calculation of the median time (see updateMedianInjectionTime()). Both could be modified after combine by calling updateConditionNames() (with modified sampleColumns argument) and updateMedianInjectionTime() (with modified by argument).

• conditionData(AbstractTopDownSet): Accessor for the colData slot.

  An alias for colData.

• conditionData(AbstractTopDownSet) <- value: Setter for the colData slot.

  An alias for ⁠colData<-⁠.

• conditionNames(AbstractTopDownSet): Accessor for condition names.

  Returns a character with names for the conditions/runs (columns).

• dim(AbstractTopDownSet): Accessor for dimensions.

  Returns a numeric with number of fragments/bonds (rows) and conditions/runs (columns).

• dimnames(AbstractTopDownSet): Accessor for dimension names.

  Returns a list with names for the fragments/bonds (rows) and for the conditions/runs (columns).

• removeEmptyConditions(AbstractTopDownSet): Remove empty conditions/runs.

  Removes conditions/runs (columns) without any intensity/coverage information from the AbstractTopDownSet object. It returns a modified AbstractTopDownSet object.

• rowViews(AbstractTopDownSet): Accessor for the rowViews slot.

  Depending on the implementation it returns an FragmentViews object for TopDownSet objects or an Biostrings::XStringViews object for NCBSet objects.

• summary(AbstractTopDownSet): Summary statistics.

  Returns a matrix with some statistics: number of fragments, total/min/first quartile/median/mean/third quartile/maximum of intensity values.

• updateConditionNames(AbstractTopDownSet): Update condition names.

  Updates condition names based on sampleColumns from conditionData/colData. Columns with just identical entries are ignored. This method will create/update the colData(object)$Sample column that identifies technical replicates and could be used in other methods.

• updateMedianInjectionTime(AbstractTopDownSet): Update median ion injection times.

  Recalculates median ion injection times by a user given grouping variable (default: Mz, AgcTarget). This is useful if you acquire new data and the ion injection time differs across the runs. Use the by argument to provide a list/data.frame of grouping variables, e.g. by=colData(object)[, c("Mz", "AgcTarget", "File")].

Slots

rowViews

Biostrings::XStringViews, information about fragments/bonds (name, type, sequence, mass, charge), see Biostrings::XStringViews and FragmentViews for details.

colData

S4Vectors::DataFrame, information about the MS2 experiments and the fragmentation conditions.

assay

Matrix::dgCMatrix, intensity/coverage values of the fragments/bonds. The rows correspond to the fragments/bonds and the columns to the condition/run. It just stores values that are different from zero.

files

character, files that were imported.

processing

character, log messages.

Author(s)

Sebastian Gibb [e-mail]

See Also

• TopDownSet and NCBSet which both implement/use this interface. These manual pages also provide some example code.

• FragmentViews (and Biostrings::XStringViews) for the row view interface.

• Matrix::dgCMatrix for technical details about the intensity/coverage storage.

Examples

## Because AbstractTopDownSet is a VIRTUAL class we could not create any
## object of it. Here we demonstrate the usage with an TopDownSet that
## implements the AbstractTopDownSet interface. See `?"TopDownSet-class"` for
## more details an further examples.

## Example data
data(tds, package="topdownr")

tds

head(summary(tds))

# Accessing slots
rowViews(tds)
colData(tds)
head(assayData(tds))

# Accessing colData
tds$Mz
tds$FilterString

# Subsetting

# First 100 fragments
tds[1:100]

# All c fragments
tds["c"]

# Just c 152
tds["c152"]

# Condition 1 to 10
tds[, 1:10]

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.