HybridMTest
This is the development version of HybridMTest; for the stable release version, see HybridMTest.
Hybrid Multiple Testing
Bioconductor version: Development (3.24)
Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.
Author: Stan Pounds <stanley.pounds at stjude.org>, Demba Fofana <demba.fofana at stjude.org>
Maintainer: Demba Fofana <demba.fofana at stjude.org>
citation("HybridMTest")):
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("HybridMTest")
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("HybridMTest")| Hybrid Multiple Testing | R Script | |
| Reference Manual |
Details
| biocViews | GeneExpression, Genetics, Microarray, Software |
| Version | 1.57.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 years) |
| License | GPL Version 2 or later |
| Depends | R (>= 2.9.0), Biobase, fdrtool, MASS, survival |
| Imports | stats |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | APAlyzer |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HybridMTest_1.57.0.tar.gz |
| Windows Binary (x86_64) | HybridMTest_1.57.0.zip |
| macOS Binary (big-sur-x86_64) | HybridMTest_1.57.0.tgz |
| macOS Binary (sonoma-arm64) | HybridMTest_1.57.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HybridMTest |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HybridMTest |
| Bioc Package Browser | https://code.bioconductor.org/browse/HybridMTest/ |
| Package Short Url | https://bioconductor.org/packages/HybridMTest/ |
| Package Downloads Report | Download Stats |