Welcome to the Genotype Database Framework, GT.DB

GT.DB is a database framework for efficiently managing genome-wide genotype datasets (i.e. 10⁶ or more biallelic markers, 1000s of samples), as well as underlying raw data and complex phenotype data, tightly integrated with R for analysis. It is based on components developed at Perlegen Sciences, where a similar framework was used to manage nearly 10¹¹ individual genotypes with underlying data, representing more than 100,000 samples and more than 100 experimental datasets.

The project summary page can be found here.

Getting Started

• Install the gt.db package

  install.packages("gt.db", repos="http://R-Forge.R-project.org")
  library(gt.db)
  

• Create a temporary SQLite database

  library(RSQLite)
  fname <- tempfile()
  dbh <- dbConnect(dbDriver('SQLite'), fname)
  

• Create the gt.db tables, and load up the demo datasets

  use.gt.db(dbh)
  init.gt.db(db.mode='hex')
  demo('setup.gt.demo')
  

• Explore the code examples!

  example(fetch.gt.data)
  example(fetch.pt.data)
  example(prcomp.gt.data)
  example(xyplot.gt.data)
  example(ld.plot)
  example(score.gt.data)