Bimap-envirAPI: Environment-like API for Bimap objects

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

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.

See Also

ls, exists, get, mget, eapply, contents, sample, BimapFormatting, Bimap

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)

jmacdon/AnnotationDbi documentation built on Oct. 22, 2021, 9:14 p.m.