get.ucsc.tabledef: Get SQLite UCSC table defintions, according to organism and...

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

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")

metaseqR documentation built on Nov. 8, 2020, 5:57 p.m.