Description Usage Arguments Value Note Author(s) Examples
This function connects to the EBI's Biomart service using
the package biomaRt and downloads annotation elements
(gene co-ordinates, exon co-ordinates, gene
identifications, biotypes etc.) for each of the supported
organisms. See the help page of metaseqr
for a list of supported organisms. The function downloads
annotation for an organism genes or exons.
1 2 | get.annotation(org, type, refdb="ensembl",
multic=FALSE)
|
org |
the organism for which to download annotation. |
type |
either |
refdb |
the online source to use to fetch
annotation. It can be |
multic |
a logical value indicating the
presence of multiple cores. Defaults to
|
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 Ensembl gene and exon
accessions respectively. The gene_name corresponds to
HUGO nomenclature gene names.
The data frame that is returned contains only "canonical" chromosomes for each organism. It does not contain haplotypes or random locations and does not contain chromosome M.
Panagiotis Moulos
1 2 | hg19.genes <- get.annotation("hg19","gene","ensembl")
mm9.exons <- get.annotation("mm9","exon","ucsc")
|
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