hierGWAS
This is the development version of hierGWAS; for the stable release version, see hierGWAS.
Asessing statistical significance in predictive GWA studies
Bioconductor version: Development (3.24)
Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.
Author: Laura Buzdugan
Maintainer: Laura Buzdugan <buzdugan at stat.math.ethz.ch>
citation("hierGWAS")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("hierGWAS")
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("hierGWAS")| User manual for R-Package hierGWAS | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, LinkageDisequilibrium, SNP, Software |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL-3 |
| Depends | R (>= 3.2.0) |
| Imports | fastcluster, glmnet, fmsb |
| System Requirements | |
| URL |
See More
| Suggests | BiocGenerics, RUnit, MASS |
| 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 | hierGWAS_1.43.0.tar.gz |
| Windows Binary (x86_64) | hierGWAS_1.43.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | hierGWAS_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | hierGWAS_1.43.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hierGWAS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hierGWAS |
| Bioc Package Browser | https://code.bioconductor.org/browse/hierGWAS/ |
| Package Short Url | https://bioconductor.org/packages/hierGWAS/ |
| Package Downloads Report | Download Stats |