Estimating the Proportion of True Null Hypotheses for FDR

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Documentation for package ‘pi0’ version 1.4-0

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A C D E F G H L M N P R S V Z

pi0-package Estimating the proportion of true null hypotheses and False Discovery Rates

-- A --

agjack.pi0 Averaged generalized jackknife estimate of pi0

-- C --

CBUM (Censored) Beta-Uniform mixture for p-values
clean.cdf Saving, loading or removing pre-computed conditional cdf objects from memory or disk
coef.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
convest Estimate Proportion of True Null Hypotheses

-- D --

discTMix Fit a discrete mixture of (noncentral) t-distributions
dncp Density of noncentrality parameters
dncp.nparncpp Density of noncentrality parameters
dncp.nparncpt Density of noncentrality parameters
dncp.parncpt Density of noncentrality parameters
dncp.parncpt2 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

-- E --

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

-- F --

fdr False Discovery Rate (FDR) Estimation Based on a Given Estimate of Pi0
fitted.discTMix Density evaluated at observed statistics for discTMix class
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.parncpt2 Density evaluated at observed statistics for ncpest class
fitted.sparncpt Density evaluated at observed statistics for ncpest class
fold Reflection and folding of a function about zero

-- G --

geomean Geometric mean and harmonic mean functions
gjack Generalized jackknife
grid.search Performs a grid search to minimize the objective function

-- H --

harmean Geometric mean and harmonic mean functions
histf1 Histogram estimator of p-value density evaluated at 1

-- L --

lastbin Histogram estimator of p-value density evaluated at 1
lfdr Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.CBUM Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.convest Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.default Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.discTMix Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.nparncpp Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.nparncpt Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.parncpt Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.sparncpt Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
lfdr.znormix Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
load.cdf Saving, loading or removing pre-computed conditional cdf objects from memory or disk
logLik.ncpest log likelihood from an object of class ncpest

-- M --

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

-- N --

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

-- P --

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
parncpt2 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.parncpt2 plot an object of class parncpt, i.e., parametric estiamte of noncentrality parameters
plot.sparncpt plot an object of class sparncpt, i.e., semiparametric estimate 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.
ppee Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
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.parncpt2 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

-- R --

reflect Reflection and folding of a function about zero

-- S --

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.parncpt2 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

-- V --

varB Variance of the reflected Bsplines
vcov.ncpest extract inverse Hessian matrix from ncpest class

-- Z --

znormix Normal-mixture based estimation of LFDR and pi0