Skip to contents

Get a conversion table between biological entity (BE) identifiers

Source: R/getBeIdConvTable.R
getBeIdConvTable.Rd

Get a conversion table between biological entity (BE) identifiers

Usage

getBeIdConvTable(
  from,
  to = from,
  from.source,
  to.source,
  organism,
  caseSensitive = FALSE,
  canonical = FALSE,
  restricted = TRUE,
  entity = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  limForCache = 100
)

Arguments

from

one BE or "Probe"

to

one BE or "Probe"

from.source

the from BE ID database if BE or the from probe platform if Probe

to.source

the to BE ID database if BE or the to probe platform if Probe

organism

organism name

caseSensitive

if TRUE the case of provided symbols is taken into account during the conversion and selection. This option will only affect the conversion from "Symbol" (default: caseSensitive=FALSE). All the other conversion will be case sensitive.

canonical

if TRUE, only returns the canonical "Symbol". (default: FALSE)

restricted

boolean indicating if the results should be restricted to current version of to BEID db. If FALSE former BEID are also returned: Depending on history it can take a very long time to return a very large result!

entity

boolean indicating if the technical ID of to BE 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 from IDs. If NULL (default), the result is not filtered: all from IDs are taken into account.

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.

Value

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

  • from: the from BE ID

  • to: the to BE ID

  • entity: (optional) the technical ID of to BE

  • preferred: true if "to" is the preferred identifier for the entity

See also

getHomTable, listBe, listPlatforms, listBeIdSources

Examples

if (FALSE) { # \dontrun{
getBeIdConvTable(
    from="Gene", from.source="EntrezGene",
    to.source="Ens_gene",
    organism="human"
)
} # }