Clomial-package {Clomial} | R Documentation

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

### 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.

### Details

Package: | Clomial
Type: | Package
Version: | 0.99.0
Date: | 2014-02-11
License: | GPL (>= 2)

The main function is Clomial() which requires 2 matrices Dt and Dc among its inputs. They contain the counts of the alternative allele, and the total number of processed reads, accordingly. Their rows correspond to the genomic loci, and their columns correspond to the samples. Several models should be trained using different initial values to escape from local optima, and the best one in terms of the likelihood can be chosen by choose.best() function.

### Author(s)

Habil Zare and Alex Hu

Maintainer: Habil Zare <zare@u.washington.edu>

### References

Inferring clonal composition from multiple sections of a breast cancer, Zare et al., PLoS Computational Biology 10.7 (2014): e1003703.

### See Also

`Clomial`, `choose.best`, `Clomial.iterate`, `Clomial.likelihood`, `compute.bic`, `breastCancer`

### Examples

    set.seed(1)
    data(breastCancer)
    Dc <- breastCancer$Dc
    Dt <- breastCancer$Dt
    ClomialResult <-Clomial(Dc=Dc,Dt=Dt,maxIt=20,C=4,doParal=FALSE,binomTryNum=2)
    chosen <- choose.best(models=ClomialResult$models)
    M1 <- chosen$bestModel
    print("Genotypes:")
    print(round(M1$Mu))
    print("Clone frequencies:")
    print(M1$P)

[Package Clomial version 1.23.0 Index]