recoup
for a list of supported organisms. The function downloads
annotation for an organism genes or exons. It also uses
the UCSC public database connection API to download UCSC
and RefSeq annotations.getAnnotation(org, type, refdb="ensembl", rc=NULL)
recoup
help page for details on supported organisms."gene"
or "exon"
."ensembl"
(default),
"ucsc"
or "refseq"
. In the later two
cases, an SQL connection is opened with the UCSC
public databases.NULL
(no parallelization).
It is used in the case of type="exon"
to process
the return value of the query to the UCSC Genome
Browser database.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 Ensembl gene and exon
accessions respectively. The gene_name corresponds to
HUGO nomenclature gene names.mm9.genes <- getAnnotation("mm9","gene")
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