mutoss: Unified multiple testing procedures
Version 0.1-8

The Mutoss package and accompanying mutossGUI package are designed to ease the application and comparison of multiple hypothesis testing procedures.

AuthorMuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus, Niklas Hack, Frank Konietschke, Kornelius Rohmeyer, Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Date of publication2013-02-10 16:03:37
MaintainerKornelius Rohmeyer <rohmeyer@small-projects.de>
LicenseGPL
Version0.1-8
URL http://mutoss.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("mutoss", repos="http://R-Forge.R-project.org")

Popular man pages

ftest.marginal: Marginal F test
gatherStatistics: Gathering statistics from simulation()-Object
hochberg: Hochberg (1988) step-up procedure
multiple.down: Benjamini-Krieger-Yekutieli (2006) Multi-Stage Step-Down
regwq: REGWQ - Ryan / Einot and Gabriel / Welsch test procedure...
sidak: Sidak correction
TSBKY_pi0_est: Two-step estimation method of Benjamini, Krieger and...
See all...

All man pages Function index File listing

Man pages

ABH_pi0_est: Lowest Slope Line (LSL) method of Hochberg and Benjamini for...
adaptiveBH: Benjamini-Hochberg (2000) adaptive linear step-up procedure
adaptiveSTS: Storey-Taylor-Siegmund (2004) adaptive step-up procedure
adjPValuesPlot: A function plotting adjusted p-values...
aorc: Step-up-down test based on the asymptotically optimal...
augmentation: Wrapper function to the augmentation methods of the multtest...
BH: Benjamini-Hochberg (1995) linear step-up procedure
BL: Benjamini-Liu (1999) step-down procedure
BlaRoq: Blanchard-Roquain (2008) step-up Procedure for arbitrary...
bonferroni: Bonferroni correction...
BR_pi0_est: Estimate of pi0 using the one-step Blanchard-Roquain...
BY: Benjamini-Yekutieli (2001) step-up procedure
calculateBetaAdjustment: Calculating the beta adjustment factor for the asymptotically...
compareMutoss: Functions for comparing outputs of different procedures.
ErrorControl: Class ErrorControl
fisher22_fast: Fisher (2x2) table association analysis for calculating one...
fisher22.marginal: Fisher (2x2) table association analysis for calculating all...
fisher23_fast: Fisher-type (2x3) table association analysis for calculating...
fisher23.marginal: Fisher-type (2x3) table association analysis for calculating...
ftest.marginal: Marginal F test
gao: Xin Gao's non-parametric multiple test procedure is applied...
gatherParameters: Extracts the parameters from the simulation()-Object
gatherStatistics: Gathering statistics from simulation()-Object
hochberg: Hochberg (1988) step-up procedure
holm: Holm's (1979) step-down-procedure
hommel: Hommel's (1988) step-up-procedure
indepBR: Blanchard-Roquain (2009) 1-stage adaptive step-up
jointCDF.orderedUnif: Joint cumulative distribution function of order statistics of...
linearStepUp: Linear Step Up Service Function...
multcomp.wrapper: Simultaneous confidence intervals for arbitrary parametric...
multiple.down: Benjamini-Krieger-Yekutieli (2006) Multi-Stage Step-Down
multiple.down.adjust: A service function used by multiple...
mu.test.class: Test for compatible classes for comparison...
mu.test.name: Tests if all hypotheses have the same names.
mu.test.rates: Tests that different procedures used the same error rates.
mu.test.same.data: Tests if the same pvalues were used by different procedures.
mu.test.type: Tests that different procedures use the same error types.
Mutoss: Class Mutoss
mutoss.apply: Applies a function to a Mutoss object.
MutossMethod: Class MutossMethod
mutoss.models: Mutoss Models
mutoss.plotCI: mutoss.plotCI
notterman: Notterman data set
nparcomp: Simultaneous confidence intervals for relative contrast...
nparcomp.wrapper: Simultaneous confidence intervals for relative contrast...
onesamp.marginal: Marginal one sample test
oracleBH: Bejamini-Hochberg (2000) oracle linear step-up Procedure...
paired.marginal: Marginal paired two sample test
printRejected: Internal MuTossProjekt-Function
pval2locfdr: Strimmer et al.'s fdrtool-based local fdr
pval2qval: Strimmer et al.'s fdrtool-based q-values
pValuesPlot: A function plotting p-values...
Qvalue: Storey's (2001) q-value Procedure...
ranktruncated: Rank truncated p-Value procedure...
regwq: REGWQ - Ryan / Einot and Gabriel / Welsch test procedure...
reject: reject
requireLibrary: Tries to load a package.
rom: Rom's (1990) step-up-procedure.
SD: A general step-down procedure.
sidak: Sidak correction
SidakSD: Sidak-like (1987) step-down procedure
simulation: Simulation studies
snk: Student - Newman - Keuls rejective test procedure.
storey_pi0_est: Storey-Taylor-Siegmund estimation of pi0 (finite sample...
SU: A general step-up procedure.
SUD: A general step-up-down procedure.
TSBKY_pi0_est: Two-step estimation method of Benjamini, Krieger and...
tukey.wrapper: Tukey HSD test and simultaneous confidence intervals for all...
twosamp.marginal: Marginal two sample test
two.stage: A p-value procedure which controls the FDR for independent...
twostageBR: Blanchard-Roquain (2009) 2-stage adaptive step-up...

Functions

ABH_pi0_est Man page Source code
BH Man page Source code
BL Man page Source code
BR_pi0_est Man page
BY Man page Source code
BlaRoq Man page
ErrorControl-class Man page
Mutoss-class Man page
MutossMethod Man page
MutossMethod-class Man page
Qvalue Man page
SD Man page Source code
SU Man page Source code
SUD Man page Source code
SidakSD Man page
T.Test.tumor.vs.normal Man page
TSBKY_pi0_est Man page Source code
adaptiveBH Man page
adaptiveSTS Man page
adjPValuesPlot Man page Source code
aorc Man page Source code
augmentation Man page Source code
bh.adjust Source code
bonferroni Man page Source code
calculateBetaAdjustment Man page Source code
compareMutoss Man page Source code
fisher22.marginal Man page Source code
fisher22.model Man page Source code
fisher22_fast Man page Source code
fisher23.marginal Man page Source code
fisher23.model Man page Source code
fisher23_fast Man page Source code
ftest.marginal Man page
ftest.model Man page
gao Man page Source code
gao.wrapper Man page Source code
gatherParameters Man page Source code
gatherStatistics Man page Source code
generateFunctionStack Source code
hochberg Man page
holm Man page
hommel Man page Source code
indepBR Man page
jointCDF.orderedUnif Man page Source code
linearStepUp Man page Source code
mu.compare.adjusted Man page Source code
mu.compare.critical Man page Source code
mu.compare.summary Man page Source code
mu.test.class Man page Source code
mu.test.name Man page Source code
mu.test.rates Man page Source code
mu.test.same.data Man page Source code
mu.test.type Man page Source code
multcomp.wrapper Man page Source code
multiple.down Man page Source code
multiple.down.adjust Man page Source code
mutoss.ABH_pi0_est Source code
mutoss.BH Source code
mutoss.BL Source code
mutoss.BY Source code
mutoss.TSBKY_pi0_est Source code
mutoss.aorc Source code
mutoss.apply Man page Source code
mutoss.augmentation Source code
mutoss.bonferroni Source code
mutoss.fisher22.model Source code
mutoss.fisher23.model Source code
mutoss.gao Source code
mutoss.hommel Source code
mutoss.locfdr Source code
mutoss.multcomp Source code
mutoss.multiple.down Source code
mutoss.nparcomp Source code
mutoss.onesamp.marginal Source code
mutoss.onesamp.marginal.model Source code
mutoss.onesamp.model Source code
mutoss.onesamp.multtest Source code
mutoss.onesamp.multtest.model Source code
mutoss.plotCI Man page Source code
mutoss.qvalues Source code
mutoss.regwq Source code
mutoss.rom Source code
mutoss.sidak Source code
mutoss.snk Source code
mutoss.storey_pi0_est Source code
mutoss.tukey Source code
mutoss.two.stage Source code
notterman Man page
notterman.grpLabel Man page
nparcomp Man page Source code
nparcomp.wrapper Man page Source code
onLoad Source code
onesamp.marginal Man page Source code
onesamp.model Man page Source code
onesamp.multtest Source code
oracleBH Man page
pValuesPlot Man page Source code
paired.marginal Man page
paired.model Man page
printRejected Man page Source code
pval2locfdr Man page Source code
pval2qval Man page Source code
ranktruncated Man page Source code
regwq Man page Source code
reject Man page Source code
requireLibrary Man page Source code
rom Man page Source code
sidak Man page Source code
simulation Man page Source code
snk Man page Source code
snk.wrapper Man page Source code
solve.q Source code
storey_pi0_est Man page Source code
tukey.wrapper Man page Source code
two.stage Man page Source code
two.stage.adjust Source code
twosamp.marginal Man page
twosamp.model Man page
twostageBR Man page
weightMatrix Source code

Files

data
data/notterman.grpLabel.rda
data/notterman.rda
data/T.Test.tumor.vs.normal.rda
R
R/mutoss.plotCI.R
R/Tukey.R
R/gao.R
R/MuTossObject.R
R/helperfunctions.R
R/localfdr.R
R/mutossApply.R
R/Augmentation.R
R/Rank_Truncated.R
R/REGWQ.R
R/testFunctionsForTheGUI.R
R/moreSUDprocedures.R
R/SUDProcedures.R
R/marginal.R
R/CompareObjects.R
R/wrapperFunctions.R
R/fisher.R
R/multtest.R
R/simulationList.R
R/SUD.R
R/pi0Est.R
R/onLoad.R
R/SNK.R
R/multcomp.R
R/nparcomp1.R
R/Hommel.R
NAMESPACE
tests
tests/doRUnit.R
inst
inst/unitTests
inst/unitTests/runit.example.R
inst/doc
inst/doc/simToolManual.pdf
inst/doc/quickstart.pdf
inst/doc/index.html
inst/doc/quickstart.Rnw
inst/doc/simToolVignette.pdf
inst/doc/simToolManual.actuallyRnw
inst/doc/simToolManual.Rnw
DESCRIPTION
man
man/Qvalue.Rd
man/linearStepUp.Rd
man/mu.test.same.data.Rd
man/BL.Rd
man/ABH_pi0_est.Rd
man/multiple.down.Rd
man/printRejected.Rd
man/adaptiveBH.Rd
man/compareMutoss.Rd
man/twostageBR.Rd
man/tukey.wrapper.Rd
man/TSBKY_pi0_est.Rd
man/BlaRoq.Rd
man/notterman.Rd
man/SidakSD.Rd
man/SD.Rd
man/regwq.Rd
man/ErrorControl.Rd
man/calculateBetaAdjustment.Rd
man/storey_pi0_est.Rd
man/multcomp.wrapper.Rd
man/BH.Rd
man/hochberg.Rd
man/gao.Rd
man/adaptiveSTS.Rd
man/sidak.Rd
man/mutoss.apply.Rd
man/pval2qval.Rd
man/fisher23.marginal.Rd
man/fisher22.marginal.Rd
man/multiple.down.adjust.Rd
man/hommel.Rd
man/nparcomp.Rd
man/rom.Rd
man/mu.test.name.Rd
man/ranktruncated.Rd
man/snk.Rd
man/pval2locfdr.Rd
man/pValuesPlot.Rd
man/fisher23_fast.Rd
man/mutoss.models.Rd
man/adjPValuesPlot.Rd
man/jointCDF.orderedUnif.Rd
man/two.stage.Rd
man/SU.Rd
man/SUD.Rd
man/fisher22_fast.Rd
man/BY.Rd
man/aorc.Rd
man/holm.Rd
man/bonferroni.Rd
man/paired.marginal.Rd
man/Mutoss.Rd
man/gatherStatistics.Rd
man/indepBR.Rd
man/nparcomp.wrapper.Rd
man/onesamp.marginal.Rd
man/oracleBH.Rd
man/BR_pi0_est.Rd
man/requireLibrary.Rd
man/mu.test.rates.Rd
man/mutoss.plotCI.Rd
man/simulation.Rd
man/ftest.marginal.Rd
man/MutossMethod.Rd
man/augmentation.Rd
man/mu.test.type.Rd
man/reject.Rd
man/twosamp.marginal.Rd
man/gatherParameters.Rd
man/mu.test.class.Rd
NEWS
mutoss documentation built on May 21, 2017, 3:32 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.