mutoss: Unified multiple testing procedures

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
http://mutoss.r-forge.r-project.org/

View on R-Forge

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

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

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