getGeneDescription: Get description of genes corresponding to Biological Entity...

In BED: Biological Entity Dictionary (BED)

Get description of genes corresponding to Biological Entity identifiers

Description

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

## Not run: 
getGeneDescription(
   ids=c("1438_at", "1552335_at"),
   be="Probe",
   source="GPL570",
   organism="human"
)

## End(Not run)

BED documentation built on March 7, 2023, 6:54 p.m.