get.ucsc.dbl {metaseqR} | R Documentation

## Download annotation from UCSC servers, according to organism and source

### Description

Directly downloads UCSC and RefSeq annotation files from UCSC servers to be used with metaseqR. This functionality is used when the package RMySQL is not available for some reason, e.g. Windows machines. It created an SQLite database where the same queries can be used.

### Usage

        get.ucsc.dbl(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

An SQLite database.

### Author(s)

Panagiotis Moulos

### Examples

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

[Package metaseqR version 1.30.0 Index]