dks.pvalue: Frequentist diagnostic test for multiple testing p-values.

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/dks.R

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

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Arguments

P

An m0 x B matrix of null p-values, each column corresponds to the p-values from a single simulated study.

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

dkspvalue

The double Kolmogorov-Smirnov p-value.

kspvalue

A B-vector of the Kolmogorov-Smirnov p-values one for each test.

Author(s)

Jeffrey T. Leek [email protected]

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

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  ## 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)

Bioconductor-mirror/dks documentation built on June 1, 2017, 7:36 a.m.