get.annotation {metaseqR} | R Documentation

## 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.

### Note

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.

### Author(s)

Panagiotis Moulos

### Examples

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

[Package metaseqR version 1.30.0 Index]