trio

DOI: 10.18129/B9.bioc.trio  

This package is for version 3.17 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: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("trio")

For older versions of R, please refer to the appropriate Bioconductor release.

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	3.38.0
In Bioconductor since	BioC 2.13 (R-3.0) (10 years)
License	LGPL-2
Depends	R (>= 3.0.1)
Imports	grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1)
LinkingTo
Suggests	haplo.stats, mcbiopi, splines, 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_3.38.0.tar.gz
Windows Binary	trio_3.38.0.zip
macOS Binary (x86_64)	trio_3.38.0.tgz
macOS Binary (arm64)	trio_3.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/trio
Source Repository (Developer Access)	git clone [email protected]:packages/trio
Bioc Package Browser	https://code.bioconductor.org/browse/trio/
Package Short Url	https://bioconductor.org/packages/trio/
Package Downloads Report	Download Stats