AnnotationDbi: Bimap-envirAPI – R documentation

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Bimap-envirAPI

Environment-like API for Bimap objects

Description

These methods allow the user to manipulate any Bimap object as if it was an environment. This environment-like API is provided for backward compatibility with the traditional environment-based maps.

Usage

ls(name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
     pattern, sorted = TRUE)
  exists(x, where, envir, frame, mode, inherits)
  get(x, pos, envir, mode, inherits)
  #x[[i]]
  #x$name

  ## Converting to a list
  mget(x, envir, mode, ifnotfound, inherits)
  eapply(env, FUN, ..., all.names, USE.NAMES)
  #contents(object, all.names)

  ## Additional convenience method
  sample(x, size, replace=FALSE, prob=NULL, ...)

Arguments

`name`	A Bimap object for `ls`. A key as a literal character string or a name (possibly backtick quoted) for `x$name`.
`pos, all.names, USE.NAMES, where, frame, mode, inherits`	Ignored.
`envir`	Ignored for `ls`. A Bimap object for `mget`, `get` and `exists`.
`pattern`	An optional regular expression. Only keys matching 'pattern' are returned.
`x`	The key(s) to search for for `exists`, `get` and `mget`. A Bimap object for `[[` and `x$name`. A Bimap object or an environment for `sample`.
`i`	Single key specifying the map element to extract.
`ifnotfound`	A value to be used if the key is not found. Only `NA` is currently supported.
`env`	A Bimap object.
`FUN`	The function to be applied (see original `eapply` for environments for the details).
`...`	Optional arguments to `FUN`.
`size`	Non-negative integer giving the number of map elements to choose.
`replace`	Should sampling be with replacement?
`prob`	A vector of probability weights for obtaining the elements of the map being sampled.
`sorted`	`logical(1)`. When TRUE (default), return primary keys in sorted order.

Examples

library(hgu95av2.db)
  x <- hgu95av2CHRLOC

  ls(x)[1:3]
  exists(ls(x)[1], x)
  exists("titi", x)
  get(ls(x)[1], x)
  x[[ls(x)[1]]]
  x$titi # NULL

  mget(ls(x)[1:3], x)
  eapply(x, length)
  contents(x)

  sample(x, 3)

AnnotationDbi

Manipulation of SQLite-based annotations in Bioconductor

v1.52.0

Artistic-2.0

Authors

Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li

Initial release