Package: mutoss 0.1-13

mutoss: Unified Multiple Testing Procedures

Designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying 'mutossGUI'.

Authors:MuToss Coding Team, Gilles Blanchard, Thorsten Dickhaus, Niklas Hack, Frank Konietschke, Kornelius Rohmeyer, Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft

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NEWS

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

Peer review:

Bug tracker:https://github.com/kornl/mutoss/issues

Datasets:

On CRAN:

8.36 score 4 stars 16 packages 19 scripts 3.5k downloads 9 mentions 69 exports 15 dependencies

Last updated 8 months agofrom:d72dacd510. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:ABH_pi0_estadaptiveBHadaptiveSTSadjPValuesPlotaorcaugmentationBHBLBlaRoqbonferroniBR_pi0_estBYcalculateBetaAdjustmentcompareMutossfisher22_fastfisher22.marginalfisher22.modelfisher23_fastfisher23.marginalfisher23.modelftest.marginalftest.modelgaogatherParametersgatherStatisticshochbergholmhommelindepBRjointCDF.orderedUniflinearStepUpmu.compare.adjustedmu.compare.criticalmu.compare.summarymultcomp.wrappermultiple.downmultiple.down.adjustmutoss.applymutoss.plotCInparcompnparcomp.wrapperonesamp.marginalonesamp.modeloracleBHpaired.marginalpaired.modelprintRejectedpval2locfdrpval2qvalpValuesPlotQvalueranktruncatedregwqrequireLibraryromSDsidakSidakSDsimulationsnkstorey_pi0_estSUSUDTSBKY_pi0_esttukey.wrappertwo.stagetwosamp.marginaltwosamp.modeltwostageBR

Dependencies:BiobaseBiocGenericscodetoolsgenericslatticeMASSMatrixmultcompmulttestmvtnormplotrixsandwichsurvivalTH.datazoo

MuToss Quick Start Guide

Rendered fromquickstart.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2013-12-10
Started: 2013-12-10

MuToss Simulation Tool Guide

Rendered fromsimToolManual.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2013-12-10
Started: 2013-12-10

Readme and manuals

Help Manual

Help pageTopics
Lowest Slope Line (LSL) method of Hochberg and Benjamini for estimating pi0ABH_pi0_est
Benjamini-Hochberg (2000) adaptive linear step-up procedureadaptiveBH
Storey-Taylor-Siegmund (2004) adaptive step-up procedureadaptiveSTS
A function plotting adjusted p-values...adjPValuesPlot
Step-up-down test based on the asymptotically optimal rejection curve.aorc
Wrapper function to the augmentation methods of the multtest package.augmentation
Benjamini-Hochberg (1995) linear step-up procedureBH
Benjamini-Liu (1999) step-down procedureBL
Blanchard-Roquain (2008) step-up Procedure for arbitrary dependent p-Values...BlaRoq
Bonferroni correction...bonferroni
Estimate of pi0 using the one-step Blanchard-Roquain procedureBR_pi0_est
Benjamini-Yekutieli (2001) step-up procedureBY
Calculating the beta adjustment factor for the asymptotically optimal rejection curve.calculateBetaAdjustment
Functions for comparing outputs of different procedures.compareMutoss mu.compare.adjusted mu.compare.critical mu.compare.summary
Class ErrorControlErrorControl-class
Fisher (2x2) table association analysis for calculating one (marginal) p-value...fisher22_fast
Fisher (2x2) table association analysis for calculating all marginal p-values...fisher22.marginal
Fisher-type (2x3) table association analysis for calculating one (marginal) p-value...fisher23_fast
Fisher-type (2x3) table association analysis for calculating all marginal p-values...fisher23.marginal
Marginal F testftest.marginal
Xin Gao's non-parametric multiple test procedure is applied to Data.gao gao.wrapper
Extracts the parameters from the simulation()-ObjectgatherParameters
Gathering statistics from simulation()-ObjectgatherStatistics
Hochberg (1988) step-up procedurehochberg
Holm's (1979) step-down-procedureholm
Hommel's (1988) step-up-procedurehommel
Blanchard-Roquain (2009) 1-stage adaptive step-upindepBR
Joint cumulative distribution function of order statistics of n iid. U(0,1)-distributed random variablesjointCDF.orderedUnif
Linear Step Up Service Function...linearStepUp
Test for compatible classes for comparison...mu.test.class
Tests if all hypotheses have the same names.mu.test.name
Tests that different procedures used the same error rates.mu.test.rates
Tests if the same pvalues were used by different procedures.mu.test.same.data
Tests that different procedures use the same error types.mu.test.type
Simultaneous confidence intervals for arbitrary parametric contrasts in unbalanced one-way layouts.multcomp.wrapper
Benjamini-Krieger-Yekutieli (2006) Multi-Stage Step-Downmultiple.down
A service function used by multiple...multiple.down.adjust
Class MutossMutoss-class
Applies a function to a Mutoss object.mutoss.apply
Mutoss Modelsfisher22.model fisher23.model ftest.model onesamp.model paired.model twosamp.model
mutoss.plotCImutoss.plotCI
Class MutossMethodMutossMethod MutossMethod-class
Notterman data setnotterman notterman.grpLabel T.Test.tumor.vs.normal
Simultaneous confidence intervals for relative contrast effects...nparcomp
Simultaneous confidence intervals for relative contrast effects...nparcomp.wrapper
Marginal one sample testonesamp.marginal
Bejamini-Hochberg (2000) oracle linear step-up Procedure...oracleBH
Marginal paired two sample testpaired.marginal
Internal MuTossProjekt-FunctionprintRejected
Strimmer et al.'s fdrtool-based local fdrpval2locfdr
Strimmer et al.'s fdrtool-based q-valuespval2qval
A function plotting p-values...pValuesPlot
Storey's (2001) q-value Procedure...Qvalue
Rank truncated p-Value procedure...ranktruncated
REGWQ - Ryan / Einot and Gabriel / Welsch test procedure...regwq
rejectreject
Tries to load a package.requireLibrary
Rom's (1990) step-up-procedure.rom
A general step-down procedure.SD
Sidak correctionsidak
Sidak-like (1987) step-down procedureSidakSD
Simulation studiessimulation
Student - Newman - Keuls rejective test procedure.snk snk.wrapper
Storey-Taylor-Siegmund estimation of pi0 (finite sample version)storey_pi0_est
A general step-up procedure.SU
A general step-up-down procedure.SUD
Two-step estimation method of Benjamini, Krieger and Yekutieli for estimating pi0TSBKY_pi0_est
Tukey HSD test and simultaneous confidence intervals for all pairs comparisons...tukey.wrapper
A p-value procedure which controls the FDR for independent test statistics.two.stage
Marginal two sample testtwosamp.marginal
Blanchard-Roquain (2009) 2-stage adaptive step-up...twostageBR