====== PLINK ======
PLINK is a program from the [[|Shaun Purcell]] **er al.** at the [[http://chgr.mgh.harvard.edu/|Center for Human Genetic Research]], [[http://www.mgh.harvard.edu/|Massachusetts General Hospital]].

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.   It intigrates with [[haploview]] and a graphical interface [[|gPlink]] to aid in the visualisation an anotation of results.  PLINK also integrates with [[R]] to facilitate analysis.

Key features of PLINK include

  * Excellent data handling capabilities (multiple formats supported).
  * IBD/IBS non-parametric linkage analysis.
  * Association tests for loci, hapoltypes, quantitative traits, epistasis and much more.
  * Monte-Carlo simulations for validation of results.
  * Handling of Population Stratification.
  * Analysis of Copy Number Variants (CNVs).

===== Ebuild =====
The ebuild is shown below
<code python>
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

DESCRIPTION="PLINK is a set of tools for the statistical analysis of Whole Genom
e Association Studies."
HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/"
SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip"

# License of the package.  This must match the name of file(s) in
# /usr/portage/licenses/.  For complex license combination see the developer
# docs on gentoo.org for details.
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~x86"
IUSE="R"

S="${WORKDIR}/${P}-src"

DEPEND="
        virtual/libc
        virtual/jdk"
RDEPEND="${DEPEND}
        virtual/jre
        R? ( dev-lang/R )"

src_install() {
        mkdir ${D}usr
        dobin ${PN} gPLINK.jar || die "Install failed"
}
</code>

{{:plink-1.03.ebuild.bz2|plink-1.03.ebuild}}

===== Installation instructions =====
Create a directory in your ''/usr/local/portage'' overlay, grab the ebuild, digest it and emerge it

<code bash>
# mkdir -p /usr/local/portage/sci-biology/plink
# cd /usr/local/portage/sci-biology/plink
# wget http://kimura.no-ip.org/dokuwiki/lib/exe/fetch.php?id=plink&cache=cache&media=plink-1.03.ebuild.bz2
# bunzip2 plink-1.03.ebuild.bz2
# ebuild plink-1.03.ebuild digest
# emerge -av plink
</code>

===== References ======

  * Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. //American Journal of Human Genetics//, **81** [[http://www.ncbi.nlm.nih.gov/pubmed/17701901|PubMed]][[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17701901|full article]]

===== Links =====
  * [[http://pngu.mgh.harvard.edu/~purcell/plink/|PLINK homepage]]
  * [[http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml|Plink Tutorial]]
  * [[http://pngu.mgh.harvard.edu/~purcell/|Shaun Purcell]]
  * [[http://chgr.mgh.harvard.edu/|Center for Human Genetic Research]], [[http://www.mgh.harvard.edu/|Massachusetts General Hospital]]