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: The log-densities can be interpreted as log signal-to-noise ratios. A value > 0 means higher signal than noise, and a value < 0 a higher noise than signal.

### Note

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

### Author(s)

Holger Froehlich

[Package nem version 2.58.0 Index]