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Converts BE IDs

Source: R/convBeIds.R
convBeIds.Rd

Converts BE IDs

Usage

convBeIds(
  ids,
  from,
  from.source,
  from.org,
  to,
  to.source,
  to.org,
  caseSensitive = FALSE,
  canonical = FALSE,
  prefFilter = FALSE,
  restricted = TRUE,
  recache = FALSE,
  limForCache = 2000
)

Arguments

ids

list of identifiers

from

a character corresponding to the biological entity or Probe. Guessed if not provided

from.source

a character corresponding to the ID source. Guessed if not provided

from.org

a character corresponding to the organism. Guessed if not provided

to

a character corresponding to the biological entity or Probe

to.source

a character corresponding to the ID source

to.org

a character corresponding to the organism

caseSensitive

if TRUE the case of provided symbols is taken into account during search. 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)

prefFilter

boolean indicating if the results should be filter to keep only preferred BEID of BE when they exist (default: FALSE). If there are several preferred BEID of a BE, all are kept. If there are no preferred BEID of a BE, all non-preferred BEID are kept.

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!

recache

a logical value indicating if the results should be taken from cache or recomputed

limForCache

if there are more ids 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 with the following columns:

  • from: the input IDs

  • to: the corresponding IDs in to.source

  • to.preferred: boolean indicating if the to ID is a preferred ID for the corresponding entity.

  • to.entity: the entity technical ID of the to IDs

This data.frame can be filtered in order to remove duplicated from/to.entity associations which can lead information bias. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See also

getBeIdConvTable, convBeIdLists, convDfBeIds

Examples

if (FALSE) { # \dontrun{
oriId <- c("10", "100")
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to.source="Ens_gene"
)
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to="Peptide",
   to.source="Ens_translation"
)
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to="Peptide",
   to.source="Ens_translation",
   to.org="mouse"
)
} # }