Feeding BED: Download Ensembl DB and load gene information in BED

Not exported to avoid unintended modifications of the DB.

Usage

getEnsemblGeneIds(organism, release, gv, ddir, dbCref, dbAss, canChromosomes)

Arguments

organism

character vector of 1 element corresponding to the organism of interest (e.g. "Homo sapiens")

release

the Ensembl release of interest (e.g. "83")

gv

the genome version (e.g. "38")

ddir

path to the directory where the data should be saved

dbCref

a named vector of characters providing cross-reference DB of interest. These DB are also used to find indirect ID associations.

dbAss

a named vector of characters providing associated DB of interest. Unlike the DB in dbCref parameter, these DB are not used for indirect ID associations: the IDs are only linked to Ensembl IDs.

canChromosomes

canonical chromosmomes to be considered as preferred ID (e.g. c(1:22, "X", "Y", "MT") for human)