getAnnotation {recoup} | 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 `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.

### Usage

        getAnnotation(org, type, refdb = "ensembl", ver = NULL,
            rc = NULL)

### Arguments

`org` | the organism for which to download annotation. Check the main `recoup` help page for details on supported organisms.
`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.
`ver` | the version of `org` to use as related to `refdb` or `NULL` for latest versions. See also the main `recoup` help page.
`rc` | fraction (0-1) of cores to use in a multicore system. It defaults to `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.

### 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

        mm9.genes <- getAnnotation("mm9","gene")

[Package recoup version 1.10.1 Index]