get.ensembl.annotation {metaseqR} | R Documentation

## Ensembl 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.ensembl.annotation(org, type)

### Arguments

`org` | the organism for which to download annotation.
`type` | either `"gene"` or `"exon"`.

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

[Package metaseqR version 1.28.0 Index]