clonEM: Auxiliary EM algorithm Function.

In Clonality: Clonality testing

Description

This function optimizes the likelihood of the model using an EM algorithm.

Usage

clonEM(mutmat, init.para, xigrid, conv.crit, niter)

Arguments

mutmat	Matrix containing the data, with all mutations in rows and the tumor pairs in columns. The data are coded as 0=mutation not observed, 1=shared mutation (observed in both tumors), 2=private mutation (observed in one tumor only). The first column contains the probabilities of occurence for each mutation.
init.para	Initial values of the parameters for the optimization. The order of the parameters is c(mu, sigma, pi), where mu and sigma are the mean and variance of the lognormal distribution of the random-effect xi, and pi is the proportion of clonal cases.
xigrid	Grid of the values of xi used to compute the integration; it corresponds to the domain of definition of xi.
conv.crit	Criteria used to defined convergence (on all three parameters).
niter	Maximum number of iterations used for the EM algorithm.

Value

Return the value of the parameters maximizing the likelihood, the number of iterations used, and the convergence status.

Author(s)

Audrey Mauguen [e-mail] and Venkatraman E. Seshan.

Clonality documentation built on Nov. 8, 2020, 7:45 p.m.