Fit a mixture of beta distributions in p-values | R Documentation |
Fit a mixture of beta distributions in p-values.
pval.mixbeta(p)
p |
A vector of p-values. |
The p-values are assumed to follow a mixture of two beta distributions. The null p-values follow Be(1, 1) and the non-null p-values follow Be(ξ, 1). In the first step, the proportion of true null values using Storey and Tibshirani (2003) is calculated and then MLE is adopted to obtain ξ. For more information on this see Triantafillou (2014).
A vector with the estimated π_0 and ξ values.
Michail Tsagris
R implementation and documentation: Michail Tsagris mtsagris@uoc.gr
Triantafillou S., Tsamardinos I. and Roumpelaki A. (2014). Learning neighborhoods of high confidence in constraint-based causal discovery. In European Workshop on Probabilistic Graphical Models, pp. 487-502.
Storey J.D. and Tibshirani R. (2003). Statistical significance for genome-wide experiments. Proceedings of the National Academy of Sciences, 100: 9440-9445.
pc.skel, mmhc.skel, corfs.network, local.mmhc.skel, conf.edge.lower
## simulate a dataset with continuous data y <- rdag2(400, p = 25, nei = 3) ind <- sample(1:25, 25) x <- y$x[, ind] mod <- pc.skel( x, method = "comb.fast", alpha = 0.01 ) pval <- as.vector( mod$pvalue[lower.tri(mod$pvalue)] ) pval.mixbeta(pval)
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