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| pi0-package | Estimating the proportion of true null hypotheses and False Discovery Rates |
| agjack.pi0 | Averaged generalized jackknife estimate of pi0 |
| clean.cdf | Saving, loading or removing pre-computed conditional cdf objects from memory or disk |
| coef.ncpest | Extract estimated parameters |
| coefficients.ncpest | Extract estimated parameters |
| combn2R | Randomly Choosing R Combinations of Two Groups of n and n2 Elements Taken m and m2 at a Time |
| cond.cdf | conditional cdf of p-values given noncentrality parameters |
| dncp | Density of noncentrality parameters |
| dncp.nparncpp | Density of noncentrality parameters |
| dncp.nparncpt | Density of noncentrality parameters |
| dncp.parncpt | Density of noncentrality parameters |
| dncp.sparncpt | Density of noncentrality parameters |
| dt.int2 | INTerpolation of INTeger degrees of freedom noncentral t-density |
| dt.lap | Laplace approximation to the noncentral t-density |
| dt.sad | Saddle Point Approximation of noncentral t-distribution |
| dtn.mix | Density of noncental t-normal mixture |
| extrp.pi0 | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.both | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.both.gam2 | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.gam2 | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.only | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.rate | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.rate.gam2 | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.slope | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| extrp.pi0.slope.gam2 | Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls |
| fdr | False Discovery Rate (FDR) Estimation Based on a Given Estimate of Pi0 |
| fitted.nparncpp | Density evaluated at observed statistics for ncpest class |
| fitted.nparncpt | Density evaluated at observed statistics for ncpest class |
| fitted.parncpt | Density evaluated at observed statistics for ncpest class |
| fitted.sparncpt | Density evaluated at observed statistics for ncpest class |
| fitted.values.nparncpp | Density evaluated at observed statistics for ncpest class |
| fitted.values.nparncpt | Density evaluated at observed statistics for ncpest class |
| fitted.values.parncpt | Density evaluated at observed statistics for ncpest class |
| fitted.values.sparncpt | Density evaluated at observed statistics for ncpest class |
| fold | Reflection and folding of a function about zero |
| geomean | Geometric mean and harmonic mean functions |
| gjack | Generalized jackknife |
| grid.search | Performs a grid search to minimize the objective function |
| harmean | Geometric mean and harmonic mean functions |
| histf1 | Histogram estimator of p-value density evaluated at 1 |
| lastbin | Histogram estimator of p-value density evaluated at 1 |
| load.cdf | Saving, loading or removing pre-computed conditional cdf objects from memory or disk |
| loadOrInstall | Load packages or install and load packages |
| logLik.ncpest | log likelihood from an object of class ncpest |
| marginal.dt | Estimated arginal density of t-statistics |
| marginal.dt.nparncpt | Estimated arginal density of t-statistics |
| marginal.dt.parncpt | Estimated arginal density of t-statistics |
| marginal.dt.sparncpt | Estimated arginal density of t-statistics |
| matrix.t.test | Apply a Two Sample T-test to Each Row or Column of a Matrix |
| mTruncNorm | Moments of truncated normal distribution and the integral in the noncentral t-distribution |
| mTruncNorm.int2 | Moments of truncated normal distribution and the integral in the noncentral t-distribution |
| nparncpp | Estimation of the density of absolute noncentrality parameters |
| nparncpp.iter | iterative call to the nparncpp function |
| nparncpt | Nonparametric estimation of noncentrality parameters |
| nparncpt.sqp | Nonparametric estimation of noncentrality parameters |
| parncpt | Parametric estimation of noncentrality parameter distribution |
| parncpt.bfgs.0mean | Parametric estimation of noncentrality parameter distribution |
| parncpt.bfgs.non0mean | Parametric estimation of noncentrality parameter distribution |
| parncpt.momeff | Parametric estimation of noncentrality parameter distribution |
| pavaf1 | pooling adjacent violator algorithm estimate of p-value density at 1 |
| pdf.dist | Distance between densities |
| pi0 | Estimating the proportion of true null hypotheses and False Discovery Rates |
| plot.extrpi0 | Plotting the Estimated Regression Surface |
| plot.nparncpt | plot an object of class nparncpt, i.e., nonparametric estiamte of noncentrality parameters |
| plot.parncpt | plot an object of class parncpt, i.e., parametric estiamte of noncentrality parameters |
| plot.sparncpt | plot an object of class sparncpt, i.e., semiparametric estiamte of noncentrality parameters |
| plot.subex | Plotting the P-value, Q-values, and the Regression Surface |
| plot.subt | 3D Scatter Plot of Subsample Sizes and P-value Density at One. |
| print.extrpi0 | Print the Summary of the Extrapolation |
| print.nparncpt | Print summary for an object of class nparncp |
| print.parncpt | Print summary for an object of class parncp |
| print.sparncpt | Print summary for an object of class sparncp |
| print.subex | Printing a Summary of Subsampling-Extrapolation Results |
| print.subt | Print the Summary of the Subsampling T-tests |
| pt.sad | Saddle Point Approximation of noncentral t-distribution |
| reflect | Reflection and folding of a function about zero |
| save.cdf | Saving, loading or removing pre-computed conditional cdf objects from memory or disk |
| sim.dat | Simulating a Microarray Data Set |
| simulatedDat | A Simulated Microarray Data Set |
| simulatedExtrpi0 | A Simulated 'extrpi0' Object |
| simulatedPval | t-Statistics and p-Values from a Simulated Microarray Data Set |
| simulatedSubex | A Simulated 'subex' Object |
| simulatedSubt | A Simulated 'subt' Object |
| simulatedTstat | t-Statistics and p-Values from a Simulated Microarray Data Set |
| sparncpt | Semiparametric density estimation for noncentrality parameters |
| sparncpt.nparncpt | Semiparametric density estimation for noncentrality parameters |
| sparncpt.numeric | Semiparametric density estimation for noncentrality parameters |
| sparncpt.parncpt | Semiparametric density estimation for noncentrality parameters |
| subex | Subsampling-Extrapolation Based Estimation of Proportion of True Null Hypotheses and False Discovery Rates for Microarray Data |
| subt | Subsampling a Microarray Data Set for Estimating Proportion of True Null Hypotheses |
| summary.extrpi0 | Print the Summary of the Extrapolation |
| summary.nparncpt | Print summary for an object of class nparncp |
| summary.parncpt | Print summary for an object of class parncp |
| summary.sparncpt | Print summary for an object of class sparncp |
| summary.subex | Printing a Summary of Subsampling-Extrapolation Results |
| summary.subt | Print the Summary of the Subsampling T-tests |
| varB | Variance of the reflected Bsplines |
| vcov.ncpest | extract inverse Hessian matrix from ncpest class |