get.ucsc.query {metaseqR} | R Documentation

## Return queries for the UCSC Genome Browser database, according to organism and source

### Description

Returns an SQL query to be used with a connection to the UCSC Genome Browser database and fetch metaseqR supported organism annotations. This query is constructed based on the data source and data type to be returned.

### Usage

        get.ucsc.query(org, type, refdb="ucsc")

### Arguments

`org` | one of metaseqR supported organisms.
`type` | either `"gene"` or `"exon"`.
`refdb` | one of `"ucsc"` or `"refseq"` to use the UCSC or RefSeq annotation sources respectively.

### Value

A valid SQL query.

### Author(s)

Panagiotis Moulos

### Examples

    db.query <- get.ucsc.query("hg18","gene","ucsc")

[Package metaseqR version 1.30.0 Index]