trio

DOI: 10.18129/B9.bioc.trio    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see trio.

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

Bioconductor version: 3.7

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:

## try http:// if https:// URLs are not supported
source("https://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 3.18.0
In Bioconductor since BioC 2.13 (R-3.0) (5 years)
License LGPL-2
Depends R (>= 3.0.1)
Imports
LinkingTo
Suggests survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS(>= 1.28.1), KernSmooth, VariantAnnotation
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package trio_3.18.0.tar.gz
Windows Binary trio_3.18.0.zip
Mac OS X 10.11 (El Capitan) trio_3.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/trio
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/trio
Package Short Url http://bioconductor.org/packages/trio/
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