metaseqR (version 1.12.2)

get.annotation: Annotation downloader

Description

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.

Usage

get.annotation(org, type, refdb="ensembl",
        multic=FALSE)

Arguments

org

the organism for which to download annotation.

type

either "gene" or "exon".

refdb

the online source to use to fetch annotation. It can be "ensembl" (default), "ucsc" or "refseq". In the later two cases, an SQL connection is opened with the UCSC public databases.

multic

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 Ensembl gene and exon accessions respectively. The gene_name corresponds to HUGO nomenclature gene names.

Examples

hg19.genes <- get.annotation("hg19","gene","ensembl")
mm9.exons <- get.annotation("mm9","exon","ucsc")