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.

Install the latest version of this package by entering the following in R:

```
source("https://bioconductor.org/biocLite.R")
biocLite("Clomial")
```

Author | Habil Zare and Alex Hu |

Bioconductor views | Bayesian Clustering DNASeq ExomeSeq GeneticVariability Genetics MultipleComparison Sequencing TargetedResequencing |

Date of publication | None |

Maintainer | Habil Zare <zare@txstate.edu> |

License | GPL (>= 2) |

Version | 1.10.0 |

**breastCancer:** Breast cancer data for clonal decomposition.

**choose.best:** Chooses the best trained Clomial model.

**Clomial:** Fits several binomial models to data from multiple samples of...

**Clomial1000:** Pre-computed results of Clomial.

**Clomial.generate.data:** Generates simulated data to test performance of Clomial...

**Clomial.iterate:** Runs EM iterations until convergence of the Clomial model.

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

**Clomial-package:** Fits a binomial model to data from multiple samples of a...

**compute.bic:** Computes BIC for a Clomial model.

**compute.errors:** Computes the error of a Clomial model.

DESCRIPTION

NAMESPACE

R

R/Clomial-internal.R
R/Clomial.R
R/Clomial.generate.data.R
R/Clomial.iterate.R
R/Clomial.likelihood.R
R/P2W.R
R/Phi.R
R/W2P.R
R/best.match.R
R/check.Wj.R
R/choose.best.R
R/compute.P.reparam.R
R/compute.bic.R
R/compute.errors.R
R/compute.mu.R
R/compute.q.R
R/compute.unity.states.R
R/dPdW.R
R/dPhidPcp.R
R/dPhidW.R
R/decimal2binary.R
R/normalizeQ.R
R/protect.P.R
R/reorder.clones.R
R/row.z.likelihood.R
R/rsub.R
build

build/vignette.rds

data

data/Clomial1000.rda

data/breastCancer.rda

data/datalist

inst

inst/CITATION

inst/NEWS

inst/doc

inst/doc/Clonal_decomposition_by_Clomial.R
inst/doc/Clonal_decomposition_by_Clomial.Rnw

inst/doc/Clonal_decomposition_by_Clomial.pdf

man

man/Clomial-package.Rd
man/Clomial.Rd
man/Clomial.generate.data.Rd
man/Clomial.iterate.Rd
man/Clomial.likelihood.Rd
man/Clomial1000.Rd
man/breastCancer.Rd
man/choose.best.Rd
man/compute.bic.Rd
man/compute.errors.Rd
vignettes

vignettes/Clonal_decomposition_by_Clomial.Rnw

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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