bumOptim {BioNet} | R Documentation

## Fitting a beta-uniform mixture model to p-value distribution

### Description

The function fits a beta-uniform mixture model to a given p-value distribution.

### Usage

    bumOptim(x, starts=1, labels=NULL)

### Arguments

`x` | Numerical vector of p-values, has to be named with the gene names or the gene names can be given in the labels paramater.
`starts` | Number of start points for the optimization.
`labels` | Gene names for the p-values.

### Value

List of class fb with the following elements:

`lambda` | Fitted parameter lambda for the beta-uniform mixture model.
`a` | Fitted parameter a for the beta-uniform mixture model.
`negLL` | Negative log-likelihood.
`pvalues` | P-value vector.

### Author(s)

Marcus Dittrich and Daniela Beisser

### References

M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, T. Mueller (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. (ISMB2008) Bioinformatics, 24: 13. i223-i231 Jul.

S. Pounds, S.W. Morris (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19(10): 1236-1242.

### See Also

`fitBumModel`, `plot.bum`, `hist.bum`

### Examples

    data(pvaluesExample)
    pvals <- pvaluesExample[,1]
    bum <- bumOptim(x=pvals, starts=10)
    bum

[Package BioNet version 1.40.0 Index]