bumOptim {BioNet} | R Documentation |
The function fits a beta-uniform mixture model to a given p-value distribution.
bumOptim(x, starts=1, labels=NULL)
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. |
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. |
Marcus Dittrich and Daniela Beisser
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.
fitBumModel
, plot.bum
, hist.bum
data(pvaluesExample) pvals <- pvaluesExample[,1] bum <- bumOptim(x=pvals, starts=10) bum