choose.best {Clomial} | R Documentation

## Chooses the best trained Clomial model.

### Description

Given the output of Clomial function, the likelihoods of all models are compared, and the best model is determined.

### Usage

    choose.best(models, U = NULL, PTrue = NULL, compareTo = NULL, upto =
    "All", doTalk=FALSE)

### Arguments

`models` | The models trained by `Clomial` function.
`U` | The optional genotype matrix used for comparison.
`PTrue` | The optional clone frequency matrix used for comparison.
`compareTo` | The index of the model against which all other models are compared. Set to `NULL` to disable.
`upto` | The models with index less than this value are considered. Set to "All" to include every model.
`doTalk` | If TRUE, information on number of analyzed models is reported.

### Details

If `compareTo`, `U`, and `PTrue` are `NULL` no comparison will be done, and the function runs considerably faster.

### Value

A list will be made with the following entries:

`err` | A list with 2 entries; err$P and err$U the vectors of clonal frequency errors, and genotype errors, accordingly.
`Li` | A vector of the best obtained log-likelihood for each model.
`bestInd` | The index of the best model in terms of log-likelihood.
`comparison` | If `compareTo` is not `NULL`, the result of comparison with the corresponding model is reported.
`bestModel` | The best model in terms of log-likelihood.
`seconds` | A vector of the time taken, in seconds, to train each model.

### Note

When the number of assumed clones, `C`, is greater than 6, the comparison will be time taking because all possible permutations of clones should be considered. The running time will be slowed down by `C!`.

### Author(s)

Habil Zare

### References

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

### See Also

`Clomial`, `Clomial.likelihood`, `Clomial.iterate`

### Examples

    set.seed(4)
    data(breastCancer)
    Dc <- breastCancer$Dc
    Dt <- breastCancer$Dt
    ClomialResult <-Clomial(Dc=Dc,Dt=Dt,maxIt=20,C=4,doParal=FALSE,binomTryNum=5)
    chosen <- choose.best(models=ClomialResult$models)
    M1 <- chosen$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)

[Package Clomial version 1.24.0 Index]