Clomial (version 1.8.0)

Infers clonal composition of a tumor

Description

Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.

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Version

1.8.0

License

GPL (>= 2)

Maintainer

Habil Zare

Last Published

February 15th, 2017

Functions in Clomial (1.8.0)

Clomial.iterate

Runs EM iterations until convergence of the Clomial model.

Clomial

Fits several binomial models to data from multiple samples of a single tumor.

compute.bic

Computes BIC for a Clomial model.

choose.best

Chooses the best trained Clomial model.

Clomial1000

Pre-computed results of Clomial.

compute.errors

Computes the error of a Clomial model.

Clomial-package

Fits a binomial model to data from multiple samples of a single tumor to infer its clonal decomposition.

breastCancer

Breast cancer data for clonal decomposition.

Clomial.likelihood

Computes the complete data log-likelihood of a Clomial model.

Clomial.generate.data

Generates simulated data to test performance of Clomial algorithm.