Clomial.likelihood: Computes the complete data log-likelihood of a Clomial model.
In Clomial: Infers clonal composition of a tumor

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Computes the expected complete data log-likelihood of a Clomial model over all possible values of the hidden variables.

1	Clomial.likelihood(Dc, Dt, Mu, P)

`Dt`	A matrix which contains the counts of the alternative allele where rows correspond to the genomic loci, and columns correspond to the samples.
`Dc`	A matrix which contains the counts of the total number of mapped reads where rows correspond to the genomic loci, and columns correspond to the samples.
`Mu`	The matrix which models the genotypes, where rows and columns correspond to genomic loci and clones, accordingly.
`P`	The matrix of clonal frequency where rows and columns correspond to clones and samples, accordingly.

By assuming that the genomic loci and the samples are independent given the model parameters, the computation is simplified by first summing over the samples for a locus, and then summing over all the loci. This strategy avoids exploring the exponentially huge probability space.

A list will be made with the following entries:

`ll`	The expectation of complete log-likelihood over the hidden variables.
`llS`	A vector of computed log-likelihoods at all loci.

The likelihood is computed assuming the heterozygosity is 2.

Habil Zare

Inferring clonal composition from multiple sections of a breast cancer, Zare et al., Submitted.

Clomial, choose.best, compute.bic, breastCancer

set.seed(1)
data(breastCancer)
Dc <- breastCancer$Dc
Dt <- breastCancer$Dt
ClomialResult <-Clomial(Dc=Dc,Dt=Dt,maxIt=20,C=4,doParal=FALSE,binomTryNum=1)
model1 <- ClomialResult$models[[1]]
likelihood <- Clomial.likelihood(Dc=Dc, Dt=Dt, Mu=model1$Mu, P=model1$P)$ll
print(likelihood)