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Last data update: 2014.03.03

R: Frequentist and Bayesian diagnostic tests for multiple...

dks	R Documentation

Frequentist and Bayesian diagnostic tests for multiple testing p-values.

Description

This function accepts a matrix of simulated null p-values where each column corresponds to the p-values from a single simulated study. The null p-values should represent a subset of all the simulated p-values corresponding to the tests with no signal.

Usage

  dks(P,alpha=c(0.1,10),beta=c(0.1,10),plot=TRUE,eps=1e-10)

Arguments

`P`	An m0 x B matrix of null p-values, each column corresponds to the 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.
`plot`	Should diagnostic plots be displayed.
`eps`	Maximum integration error when computing the posterior distribution.

Details

The dks function performs the Bayesian and Frequentist diagnostic tests outlined in Leek and Storey (2009). The result of the function is a double Kolmogorov-Smirnov p-value as well as posterior probability of uniformity estimates for each of the studies. The p-values should be simulated from a realistic distribution and only the null p-values should be passed to the dks function.

Value

`dkspvalue`	The double Kolmogorov-Smirnov p-value.
`postprob`	A B-vector of the posterior probability that each study's null p-values are uniform.

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) 
  
  ## Perform the diagnostic tests with plots
  dks1 <- dks(P)
  dks1$dkspvalue

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/dks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dks
> ### Title: Frequentist and Bayesian diagnostic tests for multiple testing
> ###   p-values.
> ### Aliases: dks
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
>   ## Load data
>   data(dksdata) 
>   
>   ## Perform the diagnostic tests with plots
>   dks1 <- dks(P)

Computing DKS P-value...Computing Posterior Probabilities...>   dks1$dkspvalue
[1] 0.1973107
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>