Get description of genes corresponding to Biological Entity identifiers — getGeneDescription • BED

This description can be used for annotating tables or graph based on BE IDs.

Usage

getGeneDescription(
  ids,
  be,
  source,
  organism,
  gsource = largestBeSource(be = "Gene", organism = organism, rel = "is_known_as",
    restricted = TRUE),
  limForCache = 2000
)

Arguments

ids: list of identifiers
be: one BE. Guessed if not provided
source: the BE ID database. Guessed if not provided
organism: organism name. Guessed if not provided
gsource: the source of the gene IDs to use. It's chosen automatically by default.
limForCache: The number of ids above which the description is gathered for all be IDs and cached for futur queries.

Value

a data.frame providing for each BE IDs (row.names are provided BE IDs):

id: the BE ID
gsource: the Gene ID the column name provides the source of the used identifier
symbol: the associated gene symbols
name: the associated gene names

See also

getBeIdDescription, getBeIdNames, getBeIdSymbols

Examples

if (FALSE) { # \dontrun{
getGeneDescription(
   ids=c("1438_at", "1552335_at"),
   be="Probe",
   source="GPL570",
   organism="human"
)
} # }