get.ucsc.query: Return queries for the UCSC Genome Browser database,...

Description Usage Arguments Value Author(s) Examples

View source: R/metaseqr.query.R

Description

Returns an SQL query to be used with a connection to the UCSC Genome Browser database and fetch metaseqR supported organism annotations. This query is constructed based on the data source and data type to be returned.

Usage

1
    get.ucsc.query(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

A valid SQL query.

Author(s)

Panagiotis Moulos

Examples

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

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