# Unified Multiple Testing Procedures

## Documentation for package ‘mutoss’ version 0.1-12

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ABH_pi0_est | Lowest Slope Line (LSL) method of Hochberg and Benjamini for estimating pi0
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 rejection curve.
augmentation | Wrapper function to the augmentation methods of the multtest package.
BH | Benjamini-Hochberg (1995) linear step-up procedure
BL | Benjamini-Liu (1999) step-down procedure
BlaRoq | Blanchard-Roquain (2008) step-up Procedure for arbitrary dependent p-Values...
bonferroni | Bonferroni correction...
BR_pi0_est | Estimate of pi0 using the one-step Blanchard-Roquain procedure
BY | Benjamini-Yekutieli (2001) step-up procedure
calculateBetaAdjustment | Calculating the beta adjustment factor for the asymptotically optimal rejection curve.
compareMutoss | Functions for comparing outputs of different procedures.
ErrorControl-class | Class ErrorControl
fisher22.marginal | Fisher (2x2) table association analysis for calculating all marginal p-values...
fisher22.model | Mutoss Models
fisher22_fast | Fisher (2x2) table association analysis for calculating one (marginal) p-value...
fisher23.marginal | Fisher-type (2x3) table association analysis for calculating all marginal p-values...
fisher23.model | Mutoss Models
fisher23_fast | Fisher-type (2x3) table association analysis for calculating one (marginal) p-value...
ftest.marginal | Marginal F test
ftest.model | Mutoss Models
gao | Xin Gao's non-parametric multiple test procedure is applied to Data.
gao.wrapper | Xin Gao's non-parametric multiple test procedure is applied to Data.
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 n iid. U(0,1)-distributed random variables
linearStepUp | Linear Step Up Service Function...
mu.compare.adjusted | Functions for comparing outputs of different procedures.
mu.compare.critical | Functions for comparing outputs of different procedures.
mu.compare.summary | Functions for comparing outputs of different procedures.
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.
multcomp.wrapper | Simultaneous confidence intervals for arbitrary parametric contrasts in unbalanced one-way layouts.
multiple.down | Benjamini-Krieger-Yekutieli (2006) Multi-Stage Step-Down
multiple.down.adjust | A service function used by multiple...
Mutoss-class | Class Mutoss
mutoss.apply | Applies a function to a Mutoss object.
mutoss.plotCI | mutoss.plotCI
MutossMethod | Class MutossMethod
MutossMethod-class | Class MutossMethod
notterman | Notterman data set
notterman.grpLabel | Notterman data set
nparcomp | Simultaneous confidence intervals for relative contrast effects...
nparcomp.wrapper | Simultaneous confidence intervals for relative contrast effects...
onesamp.marginal | Marginal one sample test
onesamp.model | Mutoss Models
oracleBH | Bejamini-Hochberg (2000) oracle linear step-up Procedure...
paired.marginal | Marginal paired two sample test
paired.model | Mutoss Models
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.
snk.wrapper | Student - Newman - Keuls rejective test procedure.
storey_pi0_est | Storey-Taylor-Siegmund estimation of pi0 (finite sample version)
SU | A general step-up procedure.
SUD | A general step-up-down procedure.
T.Test.tumor.vs.normal | Notterman data set
TSBKY_pi0_est | Two-step estimation method of Benjamini, Krieger and Yekutieli for estimating pi0
tukey.wrapper | Tukey HSD test and simultaneous confidence intervals for all pairs comparisons...
two.stage | A p-value procedure which controls the FDR for independent test statistics.
twosamp.marginal | Marginal two sample test
twosamp.model | Mutoss Models
twostageBR | Blanchard-Roquain (2009) 2-stage adaptive step-up...