get.ucsc.dbl: Download annotation from UCSC servers, according to organism...

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

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")

pmoulos/metaseqr documentation built on Dec. 29, 2020, 5:56 a.m.