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

Description Usage Arguments Value Author(s) Examples

View source: R/metaseqr.query.R

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

1
    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

1
db.tabledefs <- get.ucsc.tabledef("hg18","gene","ucsc")

pmoulos/metaseqR documentation built on Dec. 21, 2020, 6:19 a.m.