getDensityMatrix {nem}R Documentation

Calculate density matrix from raw p-value matrix

Description

Fit a 3 component BUM model to each column of a raw p-value matrix.

Usage

        getDensityMatrix(Porig, dirname=NULL, startab=c(0.3,10), startlam=c(0.6,0.1,0.3), tol=1e-4)

Arguments

Porig matrix of raw p-values
dirname name of a directory to save histograms and QQ-plots to. If dirname=NULL, then the plots are made to the screen, and after each fit the user is asked to press a key in order to continue.
startab start values for alpha and beta parameter
startlam start values for mixing coefficients
tol convergence tolerance: If the absolute likelihood ratio -1 becomes smaller than this value, then the EM algorithm is supposed to be converged.

Details

The BUM density model consists of 3 components: $f(x) = lambda_1 + lambda_2*dbeta(x,alpha,1) + lambda_3*dbeta(x,1,beta)$. The mixing coefficients and the parameters alpha and beta are fitted together via an EM algorithm.

Value

log-density matrix of same dimensions as Porig

Note

Note the difference to the previous package version: the LOG-density is returned now!

Author(s)

Holger Froehlich


[Package nem version 2.6.0 Index]