pprob.uniform: Bayesian 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 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

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  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 [email protected]

References

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

See Also

dks, dks.pvalue, pprob.dist,cred.set

Examples

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

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