R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Bayesian diagnostic test for multiple testing p-values.

pprob.uniform

R Documentation

Bayesian diagnostic test for multiple testing p-values.

Description

This function accepts a vector of simulated null p-values from a single simulated study. The null p-values should representa subset of all the simulated p-values corresponding to the tests with no signal.

Usage

  pprob.uniform(p,alpha=c(0.1,10),beta=c(0.1,10),eps=1e-10)

Arguments

`p`	An vector of null p-values from a single simulated study.
`alpha`	The range of the first parameter for the prior on the beta distribution.
`beta`	The range of the second parameter for the prior on the beta distribution.
`eps`	Maximum integration error when computing the posterior distribution.

Details

The pprob.uniform function calculates the posterior probability that a set of null p-values come from the uniform distribution as described in Leek and Storey (2009). The p-values should be simulated from a realistic distribution and only the null p-values should be passed to the pprob.uniform function.

Value

`pp`	The posterior probability that p is a sample from the uniform distribution.

Author(s)

Jeffrey T. Leek jleek@jhsph.edu

References

J.T. Leek and J.D. Storey, "The Joint Null Distribution of Multiple Hypothesis Tests."

Examples

  ## Load data
  data(dksdata) 
  pp <- pprob.uniform(P[,1])
  hist(pp)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(dks)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dks/pprob.uniform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pprob.uniform
> ### Title: Bayesian diagnostic test for multiple testing p-values.
> ### Aliases: pprob.uniform
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## Load data
>   data(dksdata) 
>   pp <- pprob.uniform(P[,1])
>   hist(pp)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>