Frequentist diagnostic test 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.pvalue(P)

Arguments

Details

The dks.pvalue function performs the double Kolmogorov-Smirnov test outlined 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 dks.pvalue function.

Value

Author(s)

Jeffrey T. Leek jleek@jhsph.edu

References

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

See Also

pprob.uniform, dks, pprob.dist,cred.set

Examples

  ## Load data
  data(dksdata) 

  ## Calculate the double KS p-value
  dksp <- dks.pvalue(P)
  dksp$dkspvalue

  ## Histogram of the distribution of KS test p-values
  hist(dksp$kspvalue)

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.pvalue.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dks.pvalue
> ### Title: Frequentist diagnostic test for multiple testing p-values.
> ### Aliases: dks.pvalue
> ### Keywords: misc
> 
> ### ** Examples
> 
>   ## Load data
>   data(dksdata) 
> 
>   ## Calculate the double KS p-value
>   dksp <- dks.pvalue(P)
>   dksp$dkspvalue
[1] 0.1973107
> 
>   ## Histogram of the distribution of KS test p-values
>   hist(dksp$kspvalue)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>