Clomial: Infers clonal composition of a tumor

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.

Author
Habil Zare and Alex Hu
Date of publication
None
Maintainer
Habil Zare <zare@txstate.edu>
License
GPL (>= 2)
Version
1.10.0

View on Bioconductor

Man pages

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.

Files in this package

Clomial/DESCRIPTION
Clomial/NAMESPACE
Clomial/R
Clomial/R/Clomial-internal.R
Clomial/R/Clomial.R
Clomial/R/Clomial.generate.data.R
Clomial/R/Clomial.iterate.R
Clomial/R/Clomial.likelihood.R
Clomial/R/P2W.R
Clomial/R/Phi.R
Clomial/R/W2P.R
Clomial/R/best.match.R
Clomial/R/check.Wj.R
Clomial/R/choose.best.R
Clomial/R/compute.P.reparam.R
Clomial/R/compute.bic.R
Clomial/R/compute.errors.R
Clomial/R/compute.mu.R
Clomial/R/compute.q.R
Clomial/R/compute.unity.states.R
Clomial/R/dPdW.R
Clomial/R/dPhidPcp.R
Clomial/R/dPhidW.R
Clomial/R/decimal2binary.R
Clomial/R/normalizeQ.R
Clomial/R/protect.P.R
Clomial/R/reorder.clones.R
Clomial/R/row.z.likelihood.R
Clomial/R/rsub.R
Clomial/build
Clomial/build/vignette.rds
Clomial/data
Clomial/data/Clomial1000.rda
Clomial/data/breastCancer.rda
Clomial/data/datalist
Clomial/inst
Clomial/inst/CITATION
Clomial/inst/NEWS
Clomial/inst/doc
Clomial/inst/doc/Clonal_decomposition_by_Clomial.R
Clomial/inst/doc/Clonal_decomposition_by_Clomial.Rnw
Clomial/inst/doc/Clonal_decomposition_by_Clomial.pdf
Clomial/man
Clomial/man/Clomial-package.Rd
Clomial/man/Clomial.Rd
Clomial/man/Clomial.generate.data.Rd
Clomial/man/Clomial.iterate.Rd
Clomial/man/Clomial.likelihood.Rd
Clomial/man/Clomial1000.Rd
Clomial/man/breastCancer.Rd
Clomial/man/choose.best.Rd
Clomial/man/compute.bic.Rd
Clomial/man/compute.errors.Rd
Clomial/vignettes
Clomial/vignettes/Clonal_decomposition_by_Clomial.Rnw