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.

Author
MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus, Niklas Hack, Frank Konietschke, Kornelius Rohmeyer, Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Date of publication
2013-02-10 16:03:37
Maintainer
Kornelius Rohmeyer <rohmeyer@small-projects.de>
License
GPL
Version
0.1-8
URLs

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...

Files in this package

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