Clomial1000: Pre-computed results of Clomial.
In Clomial: Infers clonal composition of a tumor

Description Usage Format Details References See Also Examples

Pre-computed results of Clomial function are provided for demo purposes. It contains 1000 trained models on counts data from multiple samples of a single primary breast cancer obtained by deep, next-generation sequencing.

1	data(Clomial1000)

Clomial1000[["models"]] is the list of trained models.

Each model is the output of Clomial.iterate() function on the breastCancer data assuming there are 4 clones.

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

Clomial, Clomial.iterate, choose.best, breastCancer

data(Clomial1000)
chosen <- choose.best(models=Clomial1000$models)
M1 <- chosen$bestModel
print("Genotypes:")
round(M1$Mu)
print("Clone frequencies:")
M1$P
bestInd <- chosen$bestInd
plot(chosen$Li,ylab="Log-likelihood",type="l")
points(x=bestInd,y=chosen$Li[bestInd],col="red",pch=19)