getAnnotation: Annotation downloader

In recoup: An R package for the creation of complex genomic profile plots

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")

recoup documentation built on Nov. 8, 2020, 6:47 p.m.