syncTable: Sync whole genome annotation tables from UCSC's server

In jeffbhasin/genomesyncr: genomesyncr: Download, Synchronize, and Parse UCSC Genome Browser Tables from R

Description

This function will create the necessary directory tree under local, download, and extract the text file data and schema for given table from the given genome. If the data already exists, the function will only re-download and re-extract if the modified dates are different between the local and remote copies.

Usage

  syncTable(genome, table, local, url = url.default)

Arguments

genome	The UCSC string specific to the genome to be downloaded (e.g. "hg19", "hg19", "mm10", etc)
table	The UCSC string specific for the table to sync (e.g. "knownGene", "kgXref", etc)
local	The root of a local directory where all files downloaded from UCSC are stored
url	The root of the remote rsync URL to download UCSC data from (set by default to rsync://hgdownload.cse.ucsc.edu/goldenPath/)

Value

Prints status of the sync to the screen. No output object.

jeffbhasin/genomesyncr documentation built on May 19, 2019, 1:45 a.m.