multtest
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see multtest.
Resampling-based multiple hypothesis testing
Bioconductor version: 3.9
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 "3.6") 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 | 2.40.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 19 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 | a4Base, aCGH, BicARE, iPAC, KCsmart, LMGene, PREDA, rain, REDseq, SAGx, siggenes, webbioc |
| Imports Me | ABarray, aCGH, adSplit, ALDEx2, anota, anota2seq, ChIPpeakAnno, IsoGeneGUI, mAPKL, metabomxtr, nethet, OCplus, phyloseq, REDseq, RTopper, singleCellTK, synapter, webbioc, xcms |
| Suggests Me | annaffy, BiocCaseStudies, ecolitk, factDesign, GGtools, GOstats, gQTLstats, GSEAlm, maigesPack, MmPalateMiRNA, pcot2, ropls, topGO |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | multtest_2.40.0.tar.gz |
| Windows Binary | multtest_2.40.0.zip |
| Mac OS X 10.11 (El Capitan) | multtest_2.40.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |