trio

This is the development version of trio; for the stable release version, see trio.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

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

Bioconductor version: Development (3.24)

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")):

Holger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski. trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies. doi:10.18129/B9.bioc.trio, R package version 3.51.0, https://bioconductor.org/packages/trio.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneticVariability, Genetics, Microarray, SNP, Software
Version	3.51.0
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	LGPL-2
Depends	R (>= 3.0.1)
Imports	grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1), data.table
System Requirements
URL

Suggests	mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	trio_3.51.0.tar.gz
Windows Binary (x86_64)	trio_3.51.0.zip
macOS Binary (big-sur-x86_64)	trio_3.51.0.tgz
macOS Binary (sonoma-arm64)	trio_3.51.0.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	https://bioconductor.org/packages/trio/
Package Downloads Report	Download Stats