get.ucsc.annotation: UCSC/RefSeq annotation downloader

In pmoulos/metaseqR-local: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

This function connects to the UCSC Genome Browser public database and downloads annotation elements (gene co-ordinates, exon co-ordinates, gene identifications etc.) for each of the supported organisms, but using UCSC instead of Ensembl. See the help page of metaseqr for a list of supported organisms. The function downloads annotation for an organism genes or exons.

Usage

    get.ucsc.annotation(org, type, refdb="ucsc",
        multic=FALSE)

Arguments

org	the organism for which to download annotation.
type	either "gene" or "exon".
refdb	either "ucsc" or "refseq".
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 UCSC or RefSeq 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. Note also that as the UCSC databases do not contain biotype classifications like Ensembl. These will be returned as NA and as a result, some quality control plots will not be available.

Author(s)

Panagiotis Moulos

Examples

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

pmoulos/metaseqR-local documentation built on May 9, 2019, 1:13 a.m.