pi0: Estimating the proportion of true null hypotheses for FDR
Version 1.3-354

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.

Browse man pages Browse package API and functions Browse package files

AuthorLong Qu
Date of publication2014-08-22 07:27:12
MaintainerLong Qu <long.qu@wright.edu>
LicenseGPL (>= 2)
Version1.3-354
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pi0", repos="http://R-Forge.R-project.org")

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

Functions

agjack.pi0 Man page
clean.cdf Man page
cond.cdf Man page
geomean Man page
gjack Man page
harmean Man page
histf1 Man page
load.cdf Man page
loadOrInstall Man page
nparncpp Man page
nparncpp.iter Man page
pavaf1 Man page
save.cdf Man page
varB Man page
CBUM Man page Source code
Hypergeometric1F1 Source code
NBsplines Man page Source code
clean.cdf Source code
coef.ncpest Man page
coefficients.ncpest Man page
combn2R Man page Source code
combn2RRepl Man page Source code
combnBt2RAllDifc Man page Source code
combnBt2Rc Man page Source code
combnBtRc Man page Source code
combnRRepl Man page Source code
cond.cdf Source code
convest Man page Source code
dFsnc.mix Man page Source code
discTMix Man page Source code
dncp Man page Source code
dncp.nparncpF Man page Source code
dncp.nparncpp Man page Source code
dncp.nparncpt Man page Source code
dncp.parncpF Man page Source code
dncp.parncpt Man page Source code
dncp.parncpt2 Man page Source code
dncp.sparncpF Man page Source code
dncp.sparncpt Man page Source code
dt.int2 Man page Source code
dt.lap Man page Source code
dt.sad Man page Source code
dtn.mix Man page Source code
extrp.pi0 Man page
extrp.pi0.both Man page Source code
extrp.pi0.both.gam2 Man page Source code
extrp.pi0.gam2 Man page Source code
extrp.pi0.only Man page Source code
extrp.pi0.rate Man page Source code
extrp.pi0.rate.gam2 Man page Source code
extrp.pi0.slope Man page Source code
extrp.pi0.slope.gam2 Man page Source code
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 Source code
geomean Source code
grid.search Man page Source code
harmean Source code
histf1 Source code
lastbin Man page
lfdr 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
lfdr2p Man page
load.cdf Source code
loadOrInstall Source code
logLik.ncpest Man page Source code
mTruncNorm Man page Source code
mTruncNorm.int2 Man page Source code
marginal.dt Man page Source code
marginal.dt.nparncpt Man page Source code
marginal.dt.parncpt Man page Source code
marginal.dt.sparncpt Man page Source code
matrix.t.test Man page
momeff.nonzeromean Man page Man page Source code
momeff.zeromean Man page Source code
nparncpF Man page Source code
nparncpF.sqp Man page Source code
nparncpp Source code
nparncpp.iter Source code
nparncpt Man page Source code
nparncpt.sqp Man page Source code
parncpF Man page Source code
parncpF.lbfgsb.central Man page Source code
parncpF.lbfgsb.noncentral Man page Source code
parncpF.unconstrained.central Man page Source code
parncpF.unconstrained.noncentral Man page Source code
parncpt Man page Source code
parncpt.bfgs.0mean Man page Source code
parncpt.bfgs.non0mean Man page Source code
parncpt.momeff Man page Source code
parncpt2 Man page Source code
parncpt2.constrOptim Source code
parncpt2.constrOptim.CD Source code
parncpt2.constrOptim.CM Source code
parncpt2.constrOptim.CMD Source code
pavaf1 Source code
pdf.dist Man page Source code
pi0 Man page
pi0-package Man page
plot.extrpi0 Man page Source code
plot.nparncpF Man page Source code
plot.nparncpt Man page Source code
plot.parncpF Man page Source code
plot.parncpt Man page Source code
plot.parncpt2 Man page Source code
plot.sparncpF Man page Source code
plot.sparncpt Man page Source code
plot.subex Man page
plot.subt Man page Source code
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 Source code
print.parncpt Man page Source code
print.parncpt2 Man page Source code
print.sparncpF Man page Source code
print.sparncpt Man page Source code
print.subex Man page
print.subt Man page
pt.sad Man page Source code
reflect Man page Source code
save.cdf Source code
sim.dat Man page Source code
simulatedDat Man page
simulatedExtrpi0 Man page
simulatedPval Man page
simulatedSubex Man page
simulatedSubt Man page
simulatedTstat Man page
sparncpF Man page Source code
sparncpF.nparncpF Man page Source code
sparncpF.numeric Man page Source code
sparncpF.parncpF Man page Source code
sparncpt Man page Source code
sparncpt.default Source code
sparncpt.nparncpt Man page Source code
sparncpt.numeric Man page Source code
sparncpt.parncpt Man page Source code
subex Man page Source code
subt Man page Source code
summary.extrpi0 Man page
summary.nparncpF Man page
summary.nparncpt Man page
summary.parncpF Man page Source code
summary.parncpt Man page Source code
summary.parncpt2 Man page Source code
summary.sparncpF Man page Source code
summary.sparncpt Man page Source code
summary.subex Man page
summary.subt Man page
varB Source code
vcov.ncpest Man page Source code
znormix Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/CBUM.R
R/NBsplines.R
R/ToDoList.R
R/agjack.pi0.R
R/clean.cdf.R
R/combn2R.R
R/combn2RRepl.R
R/combnBt2RAllDifc.R
R/combnBt2Rc.R
R/combnBtRc.R
R/combnRRepl.R
R/cond.cdf.R
R/convest.R
R/dFsnc.mix.R
R/discTMix.R
R/dncp.R
R/dtn.mix.R
R/extrp.pi0.known.gam2.R
R/extrp.pi0.master.R
R/extrp.pi0.unknown.gam2.R
R/fdr.R
R/geomean.R
R/gjack.R
R/harmean.R
R/histf1.R
R/hypergeometric1F1.R
R/int.nct.R
R/laplace.nct.R
R/lastbin.R
R/lfdr.R
R/lfdr2p.R
R/loadOrInstall.R
R/matrix.t.test.R
R/mdt.R
R/momeff.R
R/momeff.nonzeromean.R
R/momeff.zeromean.R
R/ncpest.R
R/ncpest.helpers.R
R/ncpest.iter.R
R/nparncp.R
R/nparncpF.R
R/parncp.R
R/parncp2.R
R/parncpF.R
R/pavaf1.R
R/pdf.dist.R
R/plot.extrpi0.R
R/plot.subex.R
R/plot.subt.R
R/print.extrpi0.R
R/print.subex.R
R/print.subt.R
R/reflection.R
R/saddlepoint.nct.R
R/sim.dat.R
R/sparncp.R
R/sparncpF.R
R/subex.R
R/subt.R
R/summary.extrpi0.R
R/summary.subex.R
R/summary.subt.R
R/varB.R
R/znormix.R
data
data/simulatedDat.rda
data/simulatedExtrpi0.rda
data/simulatedPval.rda
data/simulatedSubex.rda
data/simulatedSubt.rda
data/simulatedTstat.rda
man
man/CBUM.Rd
man/agjack.Rd
man/clean.cdf.Rd
man/coef.ncpest.Rd
man/combn2R.Rd
man/cond.cdf.Rd
man/convest.Rd
man/discTMix.Rd
man/dncp.Rd
man/dt.int2.Rd
man/dt.lap.Rd
man/dtn.mix.Rd
man/extrp.pi0.master.Rd
man/fdr.Rd
man/fitted.discTMix.Rd
man/fitted.nparncp.Rd
man/geomean.Rd
man/gjack.Rd
man/grid.search.Rd
man/histf1.Rd
man/lastbin.Rd
man/lfdr.Rd
man/loadOrInstall.Rd
man/logLik.ncpest.Rd
man/mTruncNorm.Rd
man/matrix.t.test.Rd
man/mdt.Rd
man/ncpest.Rd
man/ncpest.iter.Rd
man/nparncp.Rd
man/parncp.Rd
man/pavaf1.Rd
man/pdf.dist.Rd
man/pi0-internal.Rd
man/pi0-package.Rd
man/plot.extrpi0.Rd
man/plot.nparncp.Rd
man/plot.parncp.Rd
man/plot.sparncp.Rd
man/plot.subex.Rd
man/plot.subt.Rd
man/print.extrpi0.Rd
man/print.subex.Rd
man/print.subt.Rd
man/pt.sad.Rd
man/reflection.Rd
man/sim.dat.Rd
man/simulatedDat.Rd
man/simulatedExtrpi0.Rd
man/simulatedSubex.Rd
man/simulatedSubt.Rd
man/simulatedtstat.Rd
man/sparncp.Rd
man/subex.Rd
man/subt.Rd
man/summary.nparncp.Rd
man/summary.parncp.Rd
man/summary.sparncp.Rd
man/varB.Rd
man/vcov.ncpest.Rd
man/znormix.Rd
src
src/combnBt2Rc.c
src/combnBtRc.c
src/intTruncNorm.c
src/tstatwelch.c
pi0 documentation built on May 21, 2017, 12:32 a.m.