trio

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

Bioconductor version: Release (2.14)

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, Christoph Neumann, Margaret Taub, Ingo Ruczinski

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("trio")

Documentation

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

Details

biocViews GeneticVariability, Genetics, Microarray, SNP, Software
Version 3.2.0
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
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source trio_3.2.0.tar.gz
Windows Binary trio_3.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) trio_3.2.0.tgz
Mac OS X 10.9 (Mavericks)
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