prior.EgeneAttach.EB {nem} | R Documentation

## Initialize E-gene attachment prior for empirical Bayes

### Description

This function computes an initial prior for the attachment of E-genes based on observed log-pvalue densities or log-odds ratios. This prior can then be updated within an empirical Bayes procedure (MC.EMiNEM).

### Usage

    prior.EgeneAttach.EB(ratioMat)

### Arguments

`ratioMat` | data matrix with experiments in the columns (log-odds ratios or log-pvalue densities)

### Value

|E-genes| x (|S-genes| + 1) matrix with prior E-gene attachment probabilities. The last column denotes the virtual 'null' S-gene, which is there to filter E-genes that have no obvious attachment to any of the real S-genes.

### Author(s)

Theresa Niederberger, Holger Froehlich

### References

Niederberger, T.; Etzold, S.; Lidschreiber, M; Maier, K.; Martin, D.; Fr\"ohlich, H.; Cramer, P.; Tresch, A., MC Eminem Maps the Interaction Landscape of the Mediator, PLoS Comp. Biol., 2012, submitted.

### See Also

`set.default.parameters`, `nem`

### Examples

    # only for test purposes
       data("BoutrosRNAi2002")
       D <- BoutrosRNAiDens
       control = set.default.parameters(unique(colnames(D)), Pe=prior.EgeneAttach.EB(D), mcmc.nsamples=100, mcmc.nburnin=50, type="CONTmLLBayes")  # these are *not* realistic values
       res <- nem(D,inference="mc.eminem", control=control)
       if(require(Rgraphviz))
        plot(res)

[Package nem version 2.60.0 Index]