multtest
This is the development version of multtest; for the stable release version, see multtest.
Resampling-based multiple hypothesis testing
Bioconductor version: Development (3.24)
Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Maintainer: Katherine S. Pollard <katherine.pollard at gladstone.ucsf.edu>
citation("multtest")):
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("multtest")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, MultipleComparison, Software |
| Version | 2.69.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | LGPL |
| Depends | R (>= 2.10), methods, BiocGenerics, Biobase |
| Imports | survival, MASS, stats4 |
| System Requirements | |
| URL |
See More
| Suggests | snow |
| Linking To | |
| Enhances | |
| Depends On Me | aCGH, BicARE, KCsmart, PREDA, rain, REDseq, siggenes, webbioc, cp4p, DiffCorr, PCS |
| Imports Me | a4Base, ABarray, adSplit, ALDEx2, anota, BulkSignalR, ChIPpeakAnno, GUIDEseq, metabomxtr, nethet, OCplus, phyloseq, RTopper, singleCellTK, webbioc, mutoss, nlcv, pRF, Qploidy, structSSI, TcGSA |
| Suggests Me | annaffy, CAMERA, ecolitk, factDesign, GOstats, GSEAlm, ropls, topGO, xcms, cherry, POSTm |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | multtest_2.69.0.tar.gz |
| Windows Binary (x86_64) | multtest_2.69.0.zip |
| macOS Binary (big-sur-x86_64) | multtest_2.69.0.tgz |
| macOS Binary (sonoma-arm64) | multtest_2.69.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/multtest |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/multtest |
| Bioc Package Browser | https://code.bioconductor.org/browse/multtest/ |
| Package Short Url | https://bioconductor.org/packages/multtest/ |
| Package Downloads Report | Download Stats |