bedr (version 1.1.3)

query.ucsc: read a ucsc table into R

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
	)

Value

A data.frame

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

Author

Daryl Wagott

Details

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

Examples

if (FALSE) {
  query.ucsc("refGene");
  }