AbstractTopDownSet-class: The AbstractTopDownSet class
In topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

Description Usage Arguments Details Value Methods (by generic) Slots Author(s) See Also Examples

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

## 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)
)

`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.

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.

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

[: 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.
[[: Subset operator.

i could be a numeric or logical vector and subsetting is done on the condition/run (column) level.
[[<-: 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.
$<-: 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: Accessor for the assay slot.

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

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

Replaces metadata for the conditons/runs (columns) of the AbstractTopDownSet object.
combine: 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: Accessor for the colData slot.

An alias for colData.
conditionData<-: Setter for the colData slot.

An alias for colData<-.
conditionNames: Accessor for condition names.

Returns a character with names for the conditions/runs (columns).
dim: Accessor for dimensions.

Returns a numeric with number of fragments/bonds (rows) and conditions/runs (columns).
dimnames: Accessor for dimension names.

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

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

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

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.

Sebastian Gibb mail@sebastiangibb.de

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.

## 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]