multtest
Resampling-based multiple hypothesis testing
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 2.60.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19.5 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 | BicARE, KCsmart, PREDA, REDseq, aCGH, iPAC, rain, siggenes, webbioc, cp4p, DiffCorr, PCS |
| Imports Me | ABarray, ALDEx2, ChIPpeakAnno, GUIDEseq, OCplus, RTopper, SARC, SingleCellSignalR, a4Base, adSplit, anota, metabomxtr, microbiomeMarker, nethet, phyloseq, singleCellTK, synapter, webbioc, hddplot, INCATome, mutoss, nlcv, pRF, TcGSA |
| Suggests Me | CAMERA, GOstats, GSEAlm, annaffy, ecolitk, factDesign, 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_2.60.0.tar.gz |
| Windows Binary (x86_64) | multtest_2.60.0.zip (64-bit only) |
| macOS Binary (x86_64) | multtest_2.60.0.tgz |
| macOS Binary (arm64) | multtest_2.60.0.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 |