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Get biological entities identifiers

Source: R/getBeIds.R
getBeIds.Rd

Get biological entities identifiers

Usage

getBeIds(
  be = c(listBe(), "Probe"),
  source,
  organism = NA,
  restricted,
  entity = TRUE,
  attributes = NULL,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  caseSensitive = FALSE,
  limForCache = 100,
  bef = NULL
)

Arguments

be

one BE or "Probe"

source

the BE ID database or "Symbol" if BE or the probe platform if Probe

organism

organism name

restricted

boolean indicating if the results should be restricted to current version of to BEID db. If FALSE former BEID are also returned.

entity

boolean indicating if the technical ID of BE should be returned

attributes

a character vector listing attributes that should be returned.

verbose

boolean indicating if the CQL query should be displayed

recache

boolean indicating if the CQL query should be run even if the table is already in cache

filter

character vector on which to filter id. If NULL (default), the result is not filtered: all IDs are taken into account.

caseSensitive

if TRUE the case of provided symbols is taken into account. This option will only affect "Symbol" source (default: caseSensitive=FALSE).

limForCache

if there are more filter than limForCache results are collected for all IDs (beyond provided ids) and cached for futur queries. If not, results are collected only for provided ids and not cached.

bef

For internal use only

Value

a data.frame mapping BE IDs with the following fields:

  • id: the BE ID

  • preferred: true if the id is the preferred identifier for the BE

  • BE: IF entity is TRUE the technical ID of BE

  • db.version: IF be is not "Probe" and source not "Symbol" the version of the DB

  • db.deprecated: IF be is not "Probe" and source not "Symbol" a value if the BE ID is deprecated or FALSE if it's not

  • canonical: IF source is "Symbol" TRUE if the symbol is canonical

  • organism: IF be is "Probe" the organism of the targeted BE

If attributes are part of the query, additional columns for each of them. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See also

listPlatforms, listBeIdSources

Examples

if (FALSE) { # \dontrun{
beids <- getBeIds(be="Gene", source="EntrezGene", organism="human", restricted=TRUE)
} # }