Annotated class

Description

The virtual class Annotated is used to standardize the storage of metadata with a subclass.

Details

The Annotated class supports the storage of global metadata in a subclass. This is done through the metadata slot that stores a list object.

Accessors

In the following code snippets, x is an Annotated object.

metadata(x), metadata(x) <- value: Get or set the list holding arbitrary R objects as annotations. May be, and often is, empty.

Author(s)

P. Aboyoun

See Also

The Vector class, which extends Annotated directly.

Examples

showClass("Annotated")  # shows (some of) the known subclasses

## If the IRanges package was not already loaded, this will show
## more subclasses:
library(IRanges)
showClass("Annotated")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(S4Vectors)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/S4Vectors/Annotated-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Annotated-class
> ### Title: Annotated class
> ### Aliases: Annotated Annotated-class metadata metadata,Annotated-method
> ###   metadata<- metadata<-,Annotated-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> showClass("Annotated")  # shows (some of) the known subclasses
Virtual Class "Annotated" [package "S4Vectors"]

Slots:
               
Name:  metadata
Class:     list

Known Subclasses: 
Class "Vector", directly
Class "Hits", by class "Vector", distance 2
Class "SelfHits", by class "Hits", distance 3
Class "SortedByQueryHits", by class "Hits", distance 3
Class "SortedByQuerySelfHits", by class "SelfHits", distance 4
Class "Rle", by class "Vector", distance 2
Class "List", by class "Vector", distance 2
Class "SimpleList", by class "List", distance 3
Class "HitsList", by class "SimpleList", distance 4
Class "SelfHitsList", by class "HitsList", distance 5
Class "SortedByQueryHitsList", by class "HitsList", distance 5
Class "SortedByQuerySelfHitsList", by class "SelfHitsList", distance 6
Class "FilterRules", by class "SimpleList", distance 4
Class "Pairs", by class "Vector", distance 2
> 
> ## If the IRanges package was not already loaded, this will show
> ## more subclasses:
> library(IRanges)
> showClass("Annotated")
Virtual Class "Annotated" [package "S4Vectors"]

Slots:
               
Name:  metadata
Class:     list

Known Subclasses: 
Class "Vector", directly
Class "Hits", by class "Vector", distance 2
Class "SelfHits", by class "Hits", distance 3
Class "SortedByQueryHits", by class "Hits", distance 3
Class "SortedByQuerySelfHits", by class "SelfHits", distance 4
Class "Rle", by class "Vector", distance 2
Class "List", by class "Vector", distance 2
Class "SimpleList", by class "List", distance 3
Class "HitsList", by class "SimpleList", distance 4
Class "SelfHitsList", by class "HitsList", distance 5
Class "SortedByQueryHitsList", by class "HitsList", distance 5
Class "SortedByQuerySelfHitsList", by class "SelfHitsList", distance 6
Class "FilterRules", by class "SimpleList", distance 4
Class "Pairs", by class "Vector", distance 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>