getEnsemblTranscriptIds {BED}

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

Description

Not exported to avoid unintended modifications of the DB.

Usage

getEnsemblTranscriptIds(organism, release, gv, ddir, dbCref, 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.

canChromosomes

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