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pi0 (version 1.3-250)

Estimating the proportion of true null hypotheses for FDR

Description

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.

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Version

Install

install.packages('pi0')

Monthly Downloads

42

Version

1.3-250

License

GPL (>= 2)

Maintainer

Long Qu

Last Published

September 6th, 2012

Functions in pi0 (1.3-250)

combn2R

Randomly Choosing R Combinations of Two Groups of n and n2 Elements Taken m and m2 at a Time
CBUM

(Censored) Beta-Uniform mixture for p-values
agjack.pi0

Averaged generalized jackknife estimate of pi0
fdr

False Discovery Rate (FDR) Estimation Based on a Given Estimate of Pi0
dt.lap

Laplace approximation to the noncentral t-density
marginal.dt

Estimated arginal density of t-statistics
dtn.mix

Density of noncental t-normal mixture
clean.cdf, save.cdf and load.cdf

Saving, loading or removing pre-computed conditional cdf objects from memory or disk
histf1

Histogram estimator of p-value density evaluated at 1
coef.ncpest

Extract estimated parameters
simulatedSubex

A Simulated 'subex' Object
varB

Variance of the reflected Bsplines
summary.sparncpt

Print summary for an object of class sparncp
plot.parncpt

plot an object of class parncpt, i.e., parametric estiamte of noncentrality parameters
extrp.pi0

Extrapolate the Estimates of P-value Density at 1 from Subsamples to Estimate the Proportion of True Nulls
matrix.t.test

Apply a Two Sample T-test to Each Row or Column of a Matrix
lfdr and ppee

Local False Discovery Rates (lfdr), i.e., Posterior Probability of Equivalent Expression (ppee) for gene expression profiling data.
plot.subex

Plotting the P-value, Q-values, and the Regression Surface
nparncpt

Nonparametric estimation of noncentrality parameters
vcov.ncpest

extract inverse Hessian matrix from ncpest class
dncp

Density of noncentrality parameters
cond.cdf

conditional cdf of p-values given noncentrality parameters
znormix

Normal-mixture based estimation of LFDR and pi0
subt

Subsampling a Microarray Data Set for Estimating Proportion of True Null Hypotheses
summary.nparncpt

Print summary for an object of class nparncp
mTruncNorm

Moments of truncated normal distribution and the integral in the noncentral t-distribution
subex

Subsampling-Extrapolation Based Estimation of Proportion of True Null Hypotheses and False Discovery Rates for Microarray Data
grid.search

Performs a grid search to minimize the objective function
nparncpp.iter

iterative call to the nparncpp function
sim.dat

Simulating a Microarray Data Set
geomean and harmean

Geometric mean and harmonic mean functions
dt.int2

INTerpolation of INTeger degrees of freedom noncentral t-density
fitted.discTMix

Density evaluated at observed statistics for discTMix class
lastbin

Histogram estimator of p-value density evaluated at 1
gjack

Generalized jackknife
sparncpt

Semiparametric density estimation for noncentrality parameters
fitted

Density evaluated at observed statistics for ncpest class
simulatedDat

A Simulated Microarray Data Set
reflect and fold

Reflection and folding of a function about zero
plot.nparncpt

plot an object of class nparncpt, i.e., nonparametric estiamte of noncentrality parameters
print.subex

Printing a Summary of Subsampling-Extrapolation Results
pi0-package

Estimating the proportion of true null hypotheses and False Discovery Rates
simulatedExtrpi0

A Simulated 'extrpi0' Object
simulatedTstat

t-Statistics and p-Values from a Simulated Microarray Data Set
logLik.ncpest

log likelihood from an object of class ncpest
convest

Estimate Proportion of True Null Hypotheses
internal functions not to be used by users directly

internal functions not to be used by users directly
loadOrInstall

Load packages or install and load packages
summary.parncpt

Print summary for an object of class parncp
pavaf1

pooling adjacent violator algorithm estimate of p-value density at 1
parncpt

Parametric estimation of noncentrality parameter distribution
nparncpp

Estimation of the density of absolute noncentrality parameters
plot.sparncpt

plot an object of class sparncpt, i.e., semiparametric estimate of noncentrality parameters
pdf.dist

Distance between densities
dt.sad and pt.sad

Saddle Point Approximation of noncentral t-distribution
plot.subt

3D Scatter Plot of Subsample Sizes and P-value Density at One.
print.subt

Print the Summary of the Subsampling T-tests
simulatedSubt

A Simulated 'subt' Object
discTMix

Fit a discrete mixture of (noncentral) t-distributions
plot.extrpi0

Plotting the Estimated Regression Surface
print.extrpi0

Print the Summary of the Extrapolation