Get a table of biological entity (BE) identifiers and symbols

Get a table of biological entity (BE) identifiers and symbols

Usage

getBeIdSymbolTable(
  be,
  source,
  organism,
  restricted,
  entity = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL
)

Arguments

be

one BE

source

the BE ID database

organism

organism name

restricted

boolean indicating if the results should be restricted to direct symbols

entity

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

Value

a data.frame with the following fields:

• id: the from BE ID

• symbol: the BE symbol

• canonical: true if the symbol is canonical for the direct BE ID

• direct: false if the symbol is not directly associated to the BE ID

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

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

See also

getBeIdSymbols, getBeIdNameTable

Examples

if (FALSE) { # \dontrun{
getBeIdSymbolTable(
   be="Gene",
   source="EntrezGene",
   organism="human"
)
} # }