Bimap-direction: Methods for getting/setting the direction of a Bimap object,...

In Bioconductor/AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

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))

Bioconductor/AnnotationDbi documentation built on Nov. 2, 2024, 6:27 a.m.