FunctSNP-package {FunctSNP}R Documentation

FunctSNP - SNP annotation data methods and species-specific database builder

Description

This package provides functions to query species-specific annotation databases. The main use of the package is to associate SNPs to functional information. Functions are also provided to build local databases from public repositories. Pre-built databases can be downloaded using the function downloadDB.

Details

Package: FunctSNP
Type: Package
Version: 1.0-1
Date: 2009-09-10
License: GPL-3
LazyLoad: yes


A quick start to FunctSNP:
  1. Load FunctSNP: library (FunctSNP)  
  2. Download a SNP database if it is not in the library already(e.g. for Bos taurus - species code = bta) : downloadDB("bta")
  3. Set the default species, e.g. for Bos taurus: setSpecies("bta")
  4. Retrieve information for all bovine genes: allgenes <- getGenes()

Author(s)

S. J. Goodswen with contributions from N. S. Watson-Haigh, H. N. Kadarmideen and C. Gondro

Maintainer: S. J. Goodswen <Stephen.Goodswen@csiro.au>

See Also

addSpecies downloadDB getGenes getGeneID getGenesByDist getGO getHighScoreSNP getHomolo getKEGG getNearGenes getOMIA getProteins getSNPID getSNPs getTraits installedDBs makeDB setSpecies supportedSpecies userAddedSpecies


[Package FunctSNP version 1.0-1 Index]