get.ucsc.tabledef {metaseqR} | R Documentation

## Get SQLite UCSC table defintions, according to organism and source

### Description

Creates a list of UCSC Genome Browser database tables and their SQLite definitions with the purpose of creating a temporary SQLite database to be used used with metaseqR. This functionality is used when the package RMySQL is not available for some reason, e.g. Windows machines.

### Usage

        get.ucsc.tabledef(org, type, refdb="ucsc", what="queries")

### 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.
`what` | either `"queries"` for SQLite table definitions or `"fields"` for only a vector of table field names.

### Value

A list with SQLite table definitions.

### Author(s)

Panagiotis Moulos

### Examples

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

[Package metaseqR version 1.30.0 Index]