fitBumModel: Fit beta-uniform mixture model to a p-value distribution

In BioNet: Routines for the functional analysis of biological networks

Description

The function fits a beta-uniform mixture model to a given p-value distribution. The BUM method was introduced by Stan Pounds and Steve Morris to model the p-value distribution as a signal-noise decompostion. The signal component is assumed to be B(a,1)-distributed, whereas the noise component is uniform-distributed under the null hypothesis.

Usage

fitBumModel(x, plot = TRUE, starts=10)

Arguments

x	Numeric vector of p-values.
plot	Boolean value, whether to plot a histogram and qqplot of the p-values with the fitted model.
starts	Numeric value giving the number of starts for the optimization.

Value

Maximum likelihood estimator object for the fitted bum model. 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)

Daniela Beisser

References

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.

Examples

data(pvaluesExample)
pvals <- pvaluesExample[,1]
bum.mle <- fitBumModel(pvals, plot=TRUE)
bum.mle

Example output

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: RBGL
Beta-Uniform-Mixture (BUM) model

6154 pvalues fitted

Mixture parameter (lambda):	0.467
shape parameter (a): 		0.589
log-likelihood:			350.2

BioNet documentation built on Nov. 8, 2020, 5:48 p.m.