Package: multtest 2.61.0

Katherine S. Pollard

multtest: Resampling-based multiple hypothesis testing

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.

Authors:Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit

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multtest.pdf |multtest.html✨
multtest/json (API)

# Install 'multtest' in R:
install.packages('multtest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • golub - Gene expression dataset from Golub et al.
  • golub.cl - Gene expression dataset from Golub et al.
  • golub.gnames - Gene expression dataset from Golub et al.

On BioConductor:multtest-2.61.0(bioc 3.20)multtest-2.60.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

55 exports 8.20 score 6 dependencies 140 dependents 158 mentions 177 downloads

Last updated 2 months agofrom:40bc39d79a

Exports:ABH.h0as.listblockFXboot.nullboot.resamplecenter.onlycenter.scalecorr.nullcorr.TncoxYdens.estdiffmeanXdiffs.1.NEBMTPebmtp2mtpEBupdatefwer2fdrfwer2gfwerfwer2tppfpFXG.VSget.indexget.TnHsetsIC.Cor.NAIC.CorXW.NAinsert.NAlmXlmYmarg.sampmeanXmt.maxTmt.minPmt.plotmt.rawp2adjpmt.rejectmt.sample.labelmt.sample.rawpmt.sample.teststatmt.teststatmt.teststat.num.denumMTPmtp2ebmtpplotquant.transsd.maxTsd.minPss.maxTss.minPsummarytQuantTranstwowayFXupdateVScountwapply

Dependencies:BiobaseBiocGenericslatticeMASSMatrixsurvival

Readme and manuals

Help Manual

Help pageTopics
A function to perform empirical Bayes resampling-based multiple hypothesis testingEBMTP
Class "EBMTP", classes and methods for empirical Bayes multiple testing procedure outputEBMTP-class EBMTP-method
Gene expression dataset from Golub et al. (1999)golub golub.cl golub.gnames
Functions for generating guessed sets of true null hypotheses in empirical Bayes resampling-based multiple hypothesis testingABH.h0 dens.est G.VS Hsets VScount
Step-down maxT and minP multiple testing proceduresmt.maxT mt.minP
Plotting results from multiple testing proceduresmt.plot
Adjusted p-values for simple multiple testing proceduresmt.rawp2adjp
Identity and number of rejected hypothesesmt.reject
Permutation distribution of test statistics and raw (unadjusted) p-valuesmt.sample.label mt.sample.rawp mt.sample.teststat
Computing test statistics for each row of a data framemt.teststat mt.teststat.num.denum
A function to perform resampling-based multiple hypothesis testingMTP
Class "MTP", classes and methods for multiple testing procedure outputMTP-class
Methods for MTP and EBMTP objects in Package `multtest'as.list as.list,EBMTP-method as.list,MTP-method as.list-methods EBMTP-methods ebmtp2mtp ebmtp2mtp,EBMTP-method ebmtp2mtp-methods EBupdate EBupdate,EBMTP-method EBupdate-methods MTP-methods mtp2ebmtp mtp2ebmtp,MTP-method mtp2ebmtp-methods plot plot,EBMTP,ANY-method plot,MTP,ANY-method plot-methods print,EBMTP-method print,MTP-method print-methods print.MTP summary summary,EBMTP-method summary,MTP-method summary-methods update update,MTP-method update-methods [,EBMTP-method [,MTP-method [-methods