This function connects to the UCSC Genome Browser public
database and downloads annotation elements (gene
co-ordinates, exon co-ordinates, gene identifications
etc.) for each of the supported organisms, but using UCSC
instead of Ensembl. See the help page of
metaseqr for a list of supported organisms.
The function downloads annotation for an organism genes or
exons.
a logical value indicating the
presence of multiple cores. Defaults to
FALSE. Do not change it if you are not
sure whether package parallel has been loaded
or not. It is used in the case of
type="exon" to process the return value of
the query to the UCSC Genome Browser database.
Value
A data frame with the canonical (not isoforms!) genes or
exons of the requested organism. When
type="genes", the data frame has the following
columns: chromosome, start, end, gene_id, gc_content,
strand, gene_name, biotype. When type="exon" the
data frame has the following columns: chromosome, start,
end, exon_id, gene_id, strand, gene_name, biotype. The
gene_id and exon_id correspond to UCSC or RefSeq gene
and exon accessions respectively. The gene_name corresponds
to HUGO nomenclature gene names.