hierinf
This is the development version of hierinf; for the stable release version, see hierinf.
Hierarchical Inference
Bioconductor version: Development (3.24)
Tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel.
Author: Claude Renaux [aut, cre], Laura Buzdugan [aut], Markus Kalisch [aut], Peter Bühlmann [aut]
Maintainer: Claude Renaux <renaux at stat.math.ethz.ch>
citation("hierinf")):
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("hierinf")
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("hierinf")| vignette-hierinf.Rnw | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GenomeWideAssociation, LinkageDisequilibrium, Regression, SNP, Software |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | fmsb, glmnet, methods, parallel, stats |
| System Requirements | |
| URL |
See More
| Suggests | knitr, MASS, testthat |
| 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 | hierinf_1.31.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | hierinf_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | hierinf_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/hierinf |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/hierinf |
| Bioc Package Browser | https://code.bioconductor.org/browse/hierinf/ |
| Package Short Url | https://bioconductor.org/packages/hierinf/ |
| Package Downloads Report | Download Stats |