getDensityMatrix {nem} | R Documentation |
Fit a 3 component BUM model to each column of a raw p-value matrix.
getDensityMatrix(Porig, dirname="", startab=c(0.3,10), startlam=c(0.6,0.1,0.3), tol=1e-4)
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. |
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.
density matrix of same dimensions as Porig
Holger Froehlich