trio
This package is for version 3.12 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: 3.12
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("trio")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual |
Details
| biocViews | GeneticVariability, Genetics, Microarray, SNP, Software |
| Version | 3.28.0 |
| 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 | |
| URL |
See More
| Suggests | haplo.stats, 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trio_3.28.0.tar.gz |
| Windows Binary | trio_3.28.0.zip |
| macOS 10.13 (High Sierra) | trio_3.28.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |