pi0: Estimating the proportion of true null hypotheses for FDR

This package implements method(s) to (approximately unbiasedly) estimate the proportion of true null hypotheses, i.e., the pi0, when a very large number of hypotheses are simultaneously tested, especially for the purpose of (local) false discovery rate control for microarray data. It also contains functions to estimate the distribution of noncentrality parameters from a large number of parametric tests.

AuthorLong Qu
Date of publication2014-08-22 07:27:12
MaintainerLong Qu <long.qu@wright.edu>
LicenseGPL (>= 2)

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Man pages

agjack: Averaged generalized jackknife estimate of pi0

CBUM: (Censored) Beta-Uniform mixture for p-values

clean.cdf: Saving, loading or removing pre-computed conditional cdf...

coef.ncpest: Extract estimated parameters

combn2R: Randomly Choosing R Combinations of Two Groups of n and n2...

cond.cdf: conditional cdf of p-values given noncentrality parameters

convest: Estimate Proportion of True Null Hypotheses

discTMix: Fit a discrete mixture of (noncentral) t-distributions

dncp: Density of noncentrality parameters

dt.int2: INTerpolation of INTeger degrees of freedom noncentral...

dt.lap: Laplace approximation to the noncentral t-density

dtn.mix: Density of noncental t-normal mixture

extrp.pi0.master: Extrapolate the Estimates of P-value Density at 1 from...

fdr: False Discovery Rate (FDR) Estimation Based on a Given...

fitted.discTMix: Density evaluated at observed statistics for discTMix class

fitted.nparncp: Density evaluated at observed statistics for ncpest class

geomean: Geometric mean and harmonic mean functions

gjack: Generalized jackknife

grid.search: Performs a grid search to minimize the objective function

histf1: Histogram estimator of p-value density evaluated at 1

lastbin: Histogram estimator of p-value density evaluated at 1

lfdr: Local False Discovery Rates (lfdr), i.e., Posterior...

loadOrInstall: Load packages or install and load packages

logLik.ncpest: log likelihood from an object of class ncpest

matrix.t.test: Apply a Two Sample T-test to Each Row or Column of a Matrix

mdt: Estimated arginal density of t-statistics

mTruncNorm: Moments of truncated normal distribution and the integral in...

ncpest: Estimation of the density of absolute noncentrality...

ncpest.iter: iterative call to the nparncpp function

nparncp: Nonparametric estimation of noncentrality parameters

parncp: Parametric estimation of noncentrality parameter distribution

pavaf1: pooling adjacent violator algorithm estimate of p-value...

pdf.dist: Distance between densities

pi0-internal: internal functions not to be used by users directly

pi0-package: Estimating the proportion of true null hypotheses and False...

plot.extrpi0: Plotting the Estimated Regression Surface

plot.nparncp: plot an object of class nparncpt, i.e., nonparametric...

plot.parncp: plot an object of class parncpt, i.e., parametric estiamte of...

plot.sparncp: plot an object of class sparncpt, i.e., semiparametric...

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...

print.extrpi0: Print the Summary of the Extrapolation

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

reflection: Reflection and folding of a function about zero

sim.dat: Simulating a Microarray Data Set

simulatedDat: A Simulated Microarray Data Set

simulatedExtrpi0: A Simulated 'extrpi0' Object

simulatedSubex: A Simulated 'subex' Object

simulatedSubt: A Simulated 'subt' Object

simulatedtstat: t-Statistics and p-Values from a Simulated Microarray Data...

sparncp: Semiparametric density estimation for noncentrality...

subex: Subsampling-Extrapolation Based Estimation of Proportion of...

subt: Subsampling a Microarray Data Set for Estimating Proportion...

summary.nparncp: Print summary for an object of class nparncp

summary.parncp: Print summary for an object of class parncp

summary.sparncp: Print summary for an object of class sparncp

varB: Variance of the reflected Bsplines

vcov.ncpest: extract inverse Hessian matrix from ncpest class

znormix: Normal-mixture based estimation of LFDR and pi0

Files in this package

pi0/R/CBUM.R pi0/R/NBsplines.R pi0/R/ToDoList.R pi0/R/agjack.pi0.R pi0/R/clean.cdf.R pi0/R/combn2R.R pi0/R/combn2RRepl.R pi0/R/combnBt2RAllDifc.R pi0/R/combnBt2Rc.R pi0/R/combnBtRc.R pi0/R/combnRRepl.R pi0/R/cond.cdf.R pi0/R/convest.R pi0/R/dFsnc.mix.R pi0/R/discTMix.R pi0/R/dncp.R pi0/R/dtn.mix.R pi0/R/extrp.pi0.known.gam2.R pi0/R/extrp.pi0.master.R pi0/R/extrp.pi0.unknown.gam2.R pi0/R/fdr.R pi0/R/geomean.R pi0/R/gjack.R pi0/R/harmean.R pi0/R/histf1.R pi0/R/hypergeometric1F1.R pi0/R/int.nct.R pi0/R/laplace.nct.R pi0/R/lastbin.R pi0/R/lfdr.R pi0/R/lfdr2p.R pi0/R/loadOrInstall.R pi0/R/matrix.t.test.R pi0/R/mdt.R pi0/R/momeff.R pi0/R/momeff.nonzeromean.R pi0/R/momeff.zeromean.R pi0/R/ncpest.R pi0/R/ncpest.helpers.R pi0/R/ncpest.iter.R pi0/R/nparncp.R pi0/R/nparncpF.R pi0/R/parncp.R pi0/R/parncp2.R pi0/R/parncpF.R pi0/R/pavaf1.R pi0/R/pdf.dist.R pi0/R/plot.extrpi0.R pi0/R/plot.subex.R pi0/R/plot.subt.R pi0/R/print.extrpi0.R pi0/R/print.subex.R pi0/R/print.subt.R pi0/R/reflection.R pi0/R/saddlepoint.nct.R pi0/R/sim.dat.R pi0/R/sparncp.R pi0/R/sparncpF.R pi0/R/subex.R pi0/R/subt.R pi0/R/summary.extrpi0.R pi0/R/summary.subex.R pi0/R/summary.subt.R pi0/R/varB.R pi0/R/znormix.R
pi0/man/CBUM.Rd pi0/man/agjack.Rd pi0/man/clean.cdf.Rd pi0/man/coef.ncpest.Rd pi0/man/combn2R.Rd pi0/man/cond.cdf.Rd pi0/man/convest.Rd pi0/man/discTMix.Rd pi0/man/dncp.Rd pi0/man/dt.int2.Rd pi0/man/dt.lap.Rd pi0/man/dtn.mix.Rd pi0/man/extrp.pi0.master.Rd pi0/man/fdr.Rd pi0/man/fitted.discTMix.Rd pi0/man/fitted.nparncp.Rd pi0/man/geomean.Rd pi0/man/gjack.Rd pi0/man/grid.search.Rd pi0/man/histf1.Rd pi0/man/lastbin.Rd pi0/man/lfdr.Rd pi0/man/loadOrInstall.Rd pi0/man/logLik.ncpest.Rd pi0/man/mTruncNorm.Rd pi0/man/matrix.t.test.Rd pi0/man/mdt.Rd pi0/man/ncpest.Rd pi0/man/ncpest.iter.Rd pi0/man/nparncp.Rd pi0/man/parncp.Rd pi0/man/pavaf1.Rd pi0/man/pdf.dist.Rd pi0/man/pi0-internal.Rd pi0/man/pi0-package.Rd pi0/man/plot.extrpi0.Rd pi0/man/plot.nparncp.Rd pi0/man/plot.parncp.Rd pi0/man/plot.sparncp.Rd pi0/man/plot.subex.Rd pi0/man/plot.subt.Rd pi0/man/print.extrpi0.Rd pi0/man/print.subex.Rd pi0/man/print.subt.Rd pi0/man/pt.sad.Rd pi0/man/reflection.Rd pi0/man/sim.dat.Rd pi0/man/simulatedDat.Rd pi0/man/simulatedExtrpi0.Rd pi0/man/simulatedSubex.Rd pi0/man/simulatedSubt.Rd pi0/man/simulatedtstat.Rd pi0/man/sparncp.Rd pi0/man/subex.Rd pi0/man/subt.Rd pi0/man/summary.nparncp.Rd pi0/man/summary.parncp.Rd pi0/man/summary.sparncp.Rd pi0/man/varB.Rd pi0/man/vcov.ncpest.Rd pi0/man/znormix.Rd

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