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biocLite("trio")

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trio

Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Bioconductor version: Release (3.0)

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

Author: Holger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski

Maintainer: Holger Schwender <holger.schw at gmx.de>

Citation (from within R, enter citation("trio")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("trio")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("trio")

 

PDF R Script Trio Logic Regression and genotypic TDT
PDF   Reference Manual

Details

biocViews GeneticVariability, Genetics, Microarray, SNP, Software
Version 3.4.0
In Bioconductor since BioC 2.13 (R-3.0)
License LGPL-2
Depends R (>= 3.0.1)
Imports
Suggests survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS(>= 1.28.1), KernSmooth, VariantAnnotation
System Requirements
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Depends On Me
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Package Archives

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Package Source trio_3.4.0.tar.gz
Windows Binary trio_3.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) trio_3.4.0.tgz
Mac OS X 10.9 (Mavericks) trio_3.4.0.tgz
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