geneIDsToAllScopes {BED}

Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism

Description

Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism

Usage

geneIDsToAllScopes(
  geneids,
  source,
  organism,
  entities = NULL,
  orthologs = TRUE,
  canonical_symbols = TRUE
)

Arguments

geneids

a character vector of gene identifiers

source

the source of gene identifiers. Guessed if not provided

organism

the gene organism. Guessed if not provided

entities

a numeric vector of gene entity. If NULL (default), geneids, source and organism arguments are used to identify genes. Be carefull when using entities as these identifiers are not stable.

orthologs

return identifiers from orthologs

canonical_symbols

return only canonical symbols (default: TRUE).

Value

A data.frame with the following fields:

• value: the identifier

• preferred: preferred identifier for the same BE in the same scope

• be: the type of BE

• organism: the BE organism

• source: the source of the identifier

• canonical: canonical gene product (logical)

• symbol: canonical symbol of the identifier

• Gene_entity: the gene entity input

• GeneID (optional): the gene ID input

• Gene_source (optional): the gene source input

• Gene_organism (optional): the gene organism input