Clomial: Infers clonal composition of a tumor
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHabil Zare and Alex Hu
Bioconductor views Bayesian Clustering DNASeq ExomeSeq GeneticVariability Genetics MultipleComparison Sequencing TargetedResequencing
Date of publicationNone
MaintainerHabil Zare <zare@txstate.edu>
LicenseGPL (>= 2)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Clomial")

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.

Functions

Clomial Man page Source code
Clomial-package Man page
Clomial.generate.data Man page Source code
Clomial.iterate Man page Source code
Clomial.likelihood Man page Source code
Clomial1000 Man page
P2W Source code
Phi Source code
W2P Source code
best.match Source code
breastCancer Man page
check.Wj Source code
choose.best Man page Source code
compute.P.reparam Source code
compute.bic Man page Source code
compute.errors Man page Source code
compute.mu Source code
compute.q Source code
compute.unity.states Source code
dPdW Source code
dPhidPcp Source code
dPhidW Source code
decimal2binary Source code
normalizeQ Source code
protect.P Source code
reorder.clones Source code
row.z.likelihood Source code
rsub Source code

Files

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
Clomial documentation built on May 20, 2017, 10:35 p.m.