query.ucsc: read a ucsc table into R

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

read a ucsc table into R

Usage

query.ucsc(
	x,
	mirror = "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database",
	download = TRUE,
	overwrite.local = FALSE,
	columns.keep = NULL,
	verbose = TRUE
	)

Arguments

x	a ucsc data table. Include the full path including "txt.gz" extenstion to load from a local file. Note that $HOME/bedr/data will be checked first before downloading.
mirror	the ucsc mirror
download	should the data be downloaded to $HOME/bedr/data/
overwrite.local	should the local version be overwritten if it exists
columns.keep	what columns to load. this can help with very large tables where you only want 'chr,start,end'. defaults to all. you may have to check the sql for the actual column names.
verbose	more words

Details

tables can be found at http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database

Value

A data.frame

Author(s)

Daryl Wagott

Examples

## Not run: 
  query.ucsc("refGene");
  
## End(Not run)

bedr documentation built on May 2, 2019, 11:36 a.m.