| 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... |
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