multtest
Resampling-based multiple hypothesis testing
Bioconductor version: 3.23 · Package version: 2.68.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multtest")Details
| Maintainer | Katherine S. Pollard <katherine.pollard@gladstone.ucsf.edu> |
| Author | Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit |
| License | LGPL |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, Microarray, MultipleComparison, Software |
| Package Short Url | https://bioconductor.org/packages/multtest/ |
Citation
From within R, enter citation("multtest"):
Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit. multtest: Resampling-based multiple hypothesis testing. doi:10.18129/B9.bioc.multtest, R package version 2.68.0, https://bioconductor.org/packages/multtest.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | multtest_2.68.0.tar.gz |
| Windows binary (x86_64) | multtest_2.68.0.zip |
| macOS binary (arm64) | multtest_2.68.0.tgz |
| macOS binary (x86_64) | multtest_2.68.0.tgz |
Dependencies
Depends: R (>= 2.10), methods, BiocGenerics, Biobase
Imports: survival, MASS, stats4
Suggests: snow
Reverse dependencies
Depends On Me (11): aCGH, BicARE, cp4p, DiffCorr, KCsmart, PCS, PREDA, rain, REDseq, siggenes, webbioc
Imports Me (22): a4Base, ABarray, adSplit, ALDEx2, anota, anota2seq, BulkSignalR, ChIPpeakAnno, GUIDEseq, metabomxtr, mutoss, nethet, nlcv, OCplus, phyloseq, pRF, Qploidy, RTopper, singleCellTK, structSSI, TcGSA, webbioc
Suggests Me (12): annaffy, CAMERA, cherry, ecolitk, factDesign, GOstats, GSEAlm, metabodeconplus, POSTm, ropls, topGO, xcms