pi0: Estimating the Proportion of True Null Hypotheses for FDR

Methods for estimating 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.

Install the latest version of this package by entering the following in R:
AuthorLong Qu [aut, cre, ctb], Kun Liang [ctb], Yudi Pawitan [aut] (The author(s) of OCplus::tMixture, which was modified slightly leading to discTMix in this package.), Alexander Ploner [aut] (The author(s) of OCplus::tMixture, which was modified slightly leading to discTMix in this package.), Egil Ferkingstad [aut] (The author(s) of limma::convest, which was modified slightly leading to convest in this package.), Mette Langaas [aut] (The author(s) of limma::convest, which was modified slightly leading to convest in this package.), Marcus Davy [aut] (The author(s) of limma::convest, which was modified slightly leading to convest in this package.)
Date of publication2015-07-06 19:32:47
MaintainerLong Qu <long.qu@wright.edu>
LicenseGPL (>= 2)

View on CRAN

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...

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


agjack.pi0 Man page
CBUM Man page
clean.cdf Man page
coefficients.ncpest Man page
coef.ncpest Man page
combn2R Man page
combn2RRepl Man page
combnBt2RAllDifc Man page
combnBt2Rc Man page
combnBtRc Man page
combnRRepl Man page
cond.cdf Man page
convest Man page
dFsnc.mix Man page
discTMix Man page
dncp Man page
dncp.nparncpF Man page
dncp.nparncpp Man page
dncp.nparncpt Man page
dncp.parncpF Man page
dncp.parncpt Man page
dncp.parncpt2 Man page
dncp.sparncpF Man page
dncp.sparncpt Man page
dt.int2 Man page
dt.lap Man page
dtn.mix Man page
dt.sad Man page
extrp.pi0 Man page
extrp.pi0.both Man page
extrp.pi0.both.gam2 Man page
extrp.pi0.gam2 Man page
extrp.pi0.only Man page
extrp.pi0.rate Man page
extrp.pi0.rate.gam2 Man page
extrp.pi0.slope Man page
extrp.pi0.slope.gam2 Man page
fdr Man page
fitted.discTMix Man page
fitted.nparncpF Man page
fitted.nparncpp Man page
fitted.nparncpt Man page
fitted.parncpF Man page
fitted.parncpt Man page
fitted.parncpt2 Man page
fitted.sparncpF Man page
fitted.sparncpt Man page
fitted.values.discTMix Man page
fitted.values.nparncpF Man page
fitted.values.nparncpp Man page
fitted.values.nparncpt Man page
fitted.values.parncpF Man page
fitted.values.parncpt Man page
fitted.values.sparncpF Man page
fitted.values.sparncpt Man page
fold Man page
geomean Man page
gjack Man page
grid.search Man page
harmean Man page
histf1 Man page
lastbin Man page
lfdr Man page
lfdr2p Man page
lfdr.CBUM Man page
lfdr.convest Man page
lfdr.default Man page
lfdr.discTMix Man page
lfdr.nparncpp Man page
lfdr.nparncpt Man page
lfdr.parncpt Man page
lfdr.sparncpt Man page
lfdr.znormix Man page
load.cdf Man page
logLik.ncpest Man page
marginal.dt Man page
marginal.dt.nparncpt Man page
marginal.dt.parncpt Man page
marginal.dt.sparncpt Man page
matrix.t.test Man page
momeff.nonzeromean Man page
momeff.zeromean Man page
mTruncNorm Man page
mTruncNorm.int2 Man page
NBsplines Man page
nparncpF Man page
nparncpF.sqp Man page
nparncpp Man page
nparncpp.iter Man page
nparncpt Man page
nparncpt.sqp Man page
parncpF Man page
parncpF.lbfgsb.central Man page
parncpF.lbfgsb.noncentral Man page
parncpF.unconstrained.central Man page
parncpF.unconstrained.noncentral Man page
parncpt Man page
parncpt2 Man page
parncpt.bfgs.0mean Man page
parncpt.bfgs.non0mean Man page
parncpt.momeff Man page
pavaf1 Man page
pdf.dist Man page
pi0 Man page
pi0-package Man page
plot.extrpi0 Man page
plot.nparncpF Man page
plot.nparncpt Man page
plot.parncpF Man page
plot.parncpt Man page
plot.parncpt2 Man page
plot.sparncpF Man page
plot.sparncpt Man page
plot.subex Man page
plot.subt Man page
ppee Man page
ppee.CBUM Man page
ppee.convest Man page
ppee.default Man page
ppee.discTMix Man page
ppee.nparncpp Man page
ppee.nparncpt Man page
ppee.parncpt Man page
ppee.sparncpt Man page
ppee.znormix Man page
print.extrpi0 Man page
print.nparncpF Man page
print.nparncpt Man page
print.parncpF Man page
print.parncpt Man page
print.parncpt2 Man page
print.sparncpF Man page
print.sparncpt Man page
print.subex Man page
print.subt Man page
pt.sad Man page
reflect Man page
save.cdf Man page
sim.dat Man page
simulatedDat Man page
simulatedExtrpi0 Man page
simulatedPval Man page
simulatedSubex Man page
simulatedSubt Man page
simulatedTstat Man page
sparncpF Man page
sparncpF.nparncpF Man page
sparncpF.numeric Man page
sparncpF.parncpF Man page
sparncpt Man page
sparncpt.nparncpt Man page
sparncpt.numeric Man page
sparncpt.parncpt Man page
subex Man page
subt Man page
summary.extrpi0 Man page
summary.nparncpF Man page
summary.nparncpt Man page
summary.parncpF Man page
summary.parncpt Man page
summary.parncpt2 Man page
summary.sparncpF Man page
summary.sparncpt Man page
summary.subex Man page
summary.subt Man page
varB Man page
vcov.ncpest Man page
znormix Man page


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