Lists all the databases taken into account in the BED database for a biological entity (BE)

Lists all the databases taken into account in the BED database for a biological entity (BE)

Usage

listBeIdSources(
  be = listBe(),
  organism,
  direct = FALSE,
  rel = NA,
  restricted = FALSE,
  recache = FALSE,
  verbose = FALSE,
  exclude = c()
)

Arguments

be

the BE on which to focus

organism

the name of the organism to focus on.

direct

a logical value indicating if only "direct" BE identifiers should be considered

rel

a type of relationship to consider in the query (e.g. "is_member_of") in order to focus on specific information. If NA (default) all be are taken into account whatever their available relationships.

restricted

boolean indicating if the results should be restricted to current version of to BEID db. If FALSE former BEID are also returned. There is no impact if direct is set to TRUE.

recache

boolean indicating if the CQL query should be run even if the table is already in cache

verbose

boolean indicating if the CQL query should be shown.

exclude

database to exclude from possible selection. Used to filter out technical database names such as "BEDTech_gene" and "BEDTech_transcript" used to manage orphan IDs (not linked to any gene based on information taken from sources)

Value

A data.frame indicating the number of ID in each available database with the following fields:

• database: the database name

• nbBe: number of distinct entities

• nbId: number of identifiers

• be: the BE under focus

See also

listBe, largestBeSource

Examples

if (FALSE) { # \dontrun{
listBeIdSources(be="Transcript", organism="mouse")
} # }