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trio

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


Bioconductor version: Release (3.18)

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 (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")
Trio Logic Regression and genotypic TDT PDF R Script
Reference Manual PDF

Details

biocViews GeneticVariability, Genetics, Microarray, SNP, Software
Version 3.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License LGPL-2
Depends R (>= 3.0.1)
Imports grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1)
System Requirements
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Suggests haplo.stats, mcbiopi, splines, logicFS(>= 1.28.1), KernSmooth, VariantAnnotation
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Package Archives

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

Source Package trio_3.40.0.tar.gz
Windows Binary trio_3.40.0.zip
macOS Binary (x86_64) trio_3.40.0.tgz
macOS Binary (arm64) trio_3.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/trio
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/trio
Bioc Package Browser https://code.bioconductor.org/browse/trio/
Package Short Url https://bioconductor.org/packages/trio/
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