Bimap-direction {AnnotationDbi} | R Documentation

## Methods for getting/setting the direction of a Bimap object, and undirected methods for getting/counting/setting its keys

### Description

These methods are part of the Bimap interface (see `?Bimap` for a quick overview of the Bimap objects and their interface).

They are divided in 2 groups: (1) methods for getting or setting the direction of a Bimap object and (2) methods for getting, counting or setting the left or right keys (or mapped keys only) of a Bimap object. Note that all the methods in group (2) are undirected methods i.e. what they return does NOT depend on the direction of the map (more on this below).

### Usage

    ## Getting or setting the direction of a Bimap object
    direction(x)
    direction(x) <- value
    revmap(x, ...)

    ## Getting, counting or setting the left or right keys (or mapped
    ## keys only) of a Bimap object
    Lkeys(x)
    Rkeys(x)
    Llength(x)
    Rlength(x)
    mappedLkeys(x)
    mappedRkeys(x)
    count.mappedLkeys(x)
    count.mappedRkeys(x)
    Lkeys(x) <- value
    Rkeys(x) <- value
    ## S4 method for signature 'Bimap'
    subset(x, Lkeys = NULL, Rkeys = NULL, drop.invalid.keys = FALSE)
    ## S4 method for signature 'AnnDbBimap'
    subset(x, Lkeys = NULL, Rkeys = NULL, drop.invalid.keys = FALSE,
        objName = NULL)

### Arguments

`x` | A Bimap object.
`value` | A single integer or character string indicating the new direction in `direction(x) <- value`. A character vector containing the new keys (must be a subset of the current keys) in `Lkeys(x) <- value` and `Rkeys(x) <- value`.
`Lkeys, Rkeys, drop.invalid.keys, objName, ...` | Extra arguments for `revmap` and `subset`. Extra argument for `revmap` can be: `objName` The name to give to the reversed map (only supported if `x` is an AnnDbBimap object). Extra arguments for `subset` can be: `Lkeys` The new Lkeys. `Rkeys` The new Rkeys. `drop.invalid.keys` If `drop.invalid.keys=FALSE` (the default), an error will be raised if the new Lkeys or Rkeys contain invalid keys i.e. keys that don't belong to the current Lkeys or Rkeys. If `drop.invalid.keys=TRUE`, invalid keys are silently dropped. `objName` The name to give to the submap (only supported if `x` is an AnnDbBimap object).

### Details

All Bimap objects have a direction which can be left-to-right (i.e. the mapping goes from the left keys to the right keys) or right-to-left (i.e. the mapping goes from the right keys to the left keys). A Bimap object `x` that maps from left to right is considered to be a direct map. Otherwise it is considered to be an indirect map (when it maps from right to left).

`direction` returns `1` on a direct map and `-1` otherwise.

The direction of `x` can be changed with `direction(x) <- value` where value must be `1` or `-1`. An easy way to reverse a map (i.e. to change its direction) is to do `direction(x) <- - direction(x)`, or, even better, to use `revmap(x)` which is actually the recommended way for doing it.

The `Lkeys` and `Rkeys` methods return respectively the left and right keys of a Bimap object. Unlike the `keys` method (see `?keys` for more information), these methods are direction-independent i.e. what they return does NOT depend on the direction of the map. Such methods are also said to be "undirected methods" and methods like the `keys` method are said to be "directed methods".

All the methods described below are also "undirected methods".

`Llength(x)` and `Rlength(x)` are equivalent to (but more efficient than) `length(Lkeys(x))` and `length(Rkeys(x))`, respectively.

The `mappedLkeys` (or `mappedRkeys`) method returns the left keys (or right keys) that are mapped to at least one right key (or one left key).

`count.mappedLkeys(x)` and `count.mappedRkeys(x)` are equivalent to (but more efficient than) `length(mappedLkeys(x))` and `length(mappedRkeys(x))`, respectively. These functions give overall summaries, if you want to know how many Rkeys correspond to a given Lkey you can use the `nhit` function.

`Lkeys(x) <- value` and `Rkeys(x) <- value` are the undirected versions of `keys(x) <- value` (see `?keys` for more information) and `subset(x, Lkeys=new_Lkeys, Rkeys=new_Rkeys)` is provided as a convenient way to reduce the sets of left and right keys in one single function call.

### Value

`1L` or `-1L` for `direction`.

A Bimap object of the same subtype as `x` for `revmap` and `subset`.

A character vector for `Lkeys`, `Rkeys`, `mappedLkeys` and `mappedRkeys`.

A single non-negative integer for `Llength`, `Rlength`, `count.mappedLkeys` and `count.mappedRkeys`.

### Author(s)

H. Pagès

### See Also

Bimap, Bimap-keys, BimapFormatting, Bimap-envirAPI, `nhit`

### Examples

      library(hgu95av2.db)
      ls(2)
      x <- hgu95av2GO
      x
      summary(x)
      direction(x)

      length(x)
      Llength(x)
      Rlength(x)

      keys(x)[1:4]
      Lkeys(x)[1:4]
      Rkeys(x)[1:4]

      count.mappedkeys(x)
      count.mappedLkeys(x)
      count.mappedRkeys(x)

      mappedkeys(x)[1:4]
      mappedLkeys(x)[1:4]
      mappedRkeys(x)[1:4]

      y <- revmap(x)
      y
      summary(y)
      direction(y)

      length(y)
      Llength(y)
      Rlength(y)

      keys(y)[1:4]
      Lkeys(y)[1:4]
      Rkeys(y)[1:4]

      ## etc...

      ## Get rid of all unmapped keys (left and right)
      z <- subset(y, Lkeys=mappedLkeys(y), Rkeys=mappedRkeys(y))

[Package AnnotationDbi version 1.54.1 Index]