getAnnotation {metaseqR2} | R Documentation

## Annotation downloader

### Description

For Ensembl based annotations, 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. For UCSC/RefSeq annotations, it connects to the respective SQL databases if the package `RMySQL` is present, otherwise it downloads flat files and build a temporary SQLite database to make the necessaru build queries. See the help page of `metaseqr2` for a list of supported organisms.

### Usage

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

### Arguments

`org` | the organism for which to download annotation (one of the supported ones).
`type` | `"gene"`, `"exon"` or `"utr"`. Same as the `countType` in `metaseqr2`.
`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 the annotation to use.
`rc` | Fraction of cores to use. Same as the `rc` in `buildAnnotationDatabase`.

### 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. When `type="utr"` the data frame has the following columns: chromosome, start, end, transcript_id, gene_id, strand, gene_name, biotype. The gene_id and exon_id correspond to Ensembl, UCSC or RefSeq gene, transcript 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

    mm9Genes <- getAnnotation("mm9","gene")

[Package metaseqR2 version 1.2.0 Index]