trio
This is the released version of trio; for the devel version, see trio.
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 3.50.0 |
| 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | trio_3.50.0.tar.gz |
| Windows Binary (x86_64) | trio_3.50.0.zip |
| macOS Binary (big-sur-x86_64) | trio_3.50.0.tgz |
| macOS Binary (sonoma-arm64) | trio_3.50.0.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 |