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.

Author
Long 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 publication
2015-07-06 19:32:47
Maintainer
Long Qu <long.qu@wright.edu>
License
GPL (>= 2)
Version
1.4-0
URLs

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

Files in this package

pi0
pi0/src
pi0/src/tstatwelch.c
pi0/src/combnBtRc.c
pi0/src/intTruncNorm.c
pi0/src/combnBt2Rc.c
pi0/NAMESPACE
pi0/data
pi0/data/simulatedDat.rda
pi0/data/simulatedSubt.rda
pi0/data/simulatedPval.rda
pi0/data/simulatedTstat.rda
pi0/data/simulatedExtrpi0.rda
pi0/data/simulatedSubex.rda
pi0/R
pi0/R/matrix.t.test.R
pi0/R/CBUM.R
pi0/R/reflection.R
pi0/R/NBsplines.R
pi0/R/plot.subex.R
pi0/R/pavaf1.R
pi0/R/parncp.R
pi0/R/parncp2.R
pi0/R/hypergeometric1F1.R
pi0/R/combnBt2Rc.R
pi0/R/subex.R
pi0/R/ncpest.R
pi0/R/sparncpF.R
pi0/R/gjack.R
pi0/R/ToDoList.R
pi0/R/extrp.pi0.unknown.gam2.R
pi0/R/summary.extrpi0.R
pi0/R/dncp.R
pi0/R/print.subt.R
pi0/R/combn2RRepl.R
pi0/R/ncpest.iter.R
pi0/R/int.nct.R
pi0/R/print.extrpi0.R
pi0/R/lfdr.R
pi0/R/summary.subex.R
pi0/R/saddlepoint.nct.R
pi0/R/combnBtRc.R
pi0/R/discTMix.R
pi0/R/cond.cdf.R
pi0/R/nparncp.R
pi0/R/znormix.R
pi0/R/nparncpF.R
pi0/R/laplace.nct.R
pi0/R/momeff.R
pi0/R/pdf.dist.R
pi0/R/extrp.pi0.master.R
pi0/R/combnBt2RAllDifc.R
pi0/R/fdr.R
pi0/R/histf1.R
pi0/R/plot.extrpi0.R
pi0/R/mdt.R
pi0/R/convest.R
pi0/R/agjack.pi0.R
pi0/R/plot.subt.R
pi0/R/lfdr2p.R
pi0/R/geomean.R
pi0/R/sparncp.R
pi0/R/combn2R.R
pi0/R/varB.R
pi0/R/lastbin.R
pi0/R/print.subex.R
pi0/R/momeff.nonzeromean.R
pi0/R/harmean.R
pi0/R/dtn.mix.R
pi0/R/sim.dat.R
pi0/R/subt.R
pi0/R/dFsnc.mix.R
pi0/R/extrp.pi0.known.gam2.R
pi0/R/momeff.zeromean.R
pi0/R/parncpF.R
pi0/R/clean.cdf.R
pi0/R/combnRRepl.R
pi0/R/summary.subt.R
pi0/R/ncpest.helpers.R
pi0/MD5
pi0/DESCRIPTION
pi0/man
pi0/man/combn2R.Rd
pi0/man/varB.Rd
pi0/man/vcov.ncpest.Rd
pi0/man/subex.Rd
pi0/man/ncpest.Rd
pi0/man/geomean.Rd
pi0/man/coef.ncpest.Rd
pi0/man/plot.sparncp.Rd
pi0/man/plot.nparncp.Rd
pi0/man/sparncp.Rd
pi0/man/znormix.Rd
pi0/man/discTMix.Rd
pi0/man/fitted.nparncp.Rd
pi0/man/simulatedExtrpi0.Rd
pi0/man/plot.subex.Rd
pi0/man/pi0-internal.Rd
pi0/man/print.extrpi0.Rd
pi0/man/dncp.Rd
pi0/man/ncpest.iter.Rd
pi0/man/pt.sad.Rd
pi0/man/simulatedSubt.Rd
pi0/man/grid.search.Rd
pi0/man/dt.lap.Rd
pi0/man/fitted.discTMix.Rd
pi0/man/reflection.Rd
pi0/man/gjack.Rd
pi0/man/convest.Rd
pi0/man/mdt.Rd
pi0/man/CBUM.Rd
pi0/man/plot.parncp.Rd
pi0/man/clean.cdf.Rd
pi0/man/matrix.t.test.Rd
pi0/man/simulatedSubex.Rd
pi0/man/plot.subt.Rd
pi0/man/mTruncNorm.Rd
pi0/man/dt.int2.Rd
pi0/man/plot.extrpi0.Rd
pi0/man/lfdr.Rd
pi0/man/pdf.dist.Rd
pi0/man/pi0-package.Rd
pi0/man/simulatedDat.Rd
pi0/man/parncp.Rd
pi0/man/sim.dat.Rd
pi0/man/dtn.mix.Rd
pi0/man/lastbin.Rd
pi0/man/extrp.pi0.master.Rd
pi0/man/agjack.Rd
pi0/man/cond.cdf.Rd
pi0/man/summary.parncp.Rd
pi0/man/print.subex.Rd
pi0/man/histf1.Rd
pi0/man/fdr.Rd
pi0/man/summary.sparncp.Rd
pi0/man/subt.Rd
pi0/man/simulatedtstat.Rd
pi0/man/summary.nparncp.Rd
pi0/man/logLik.ncpest.Rd
pi0/man/nparncp.Rd
pi0/man/print.subt.Rd
pi0/man/pavaf1.Rd