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]