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 <email@example.com>|
|License||GPL (>= 2)|
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