TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Version 1.14.0

Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.

AuthorGavin Ha, Sohrab P Shah
Bioconductor views CopyNumberVariation DNASeq ExomeSeq Genetics GenomicVariation HiddenMarkovModel Sequencing StatisticalMethod WholeGenome
Date of publicationNone
MaintainerGavin Ha <gavinha@broadinstitute.org>, Sohrab P Shah <sshah@bccrc.ca>
LicenseGPL-3
Version1.14.0
URL https://github.com/gavinha/TitanCNA
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TitanCNA")

Getting started

Package overview

Popular man pages

computeSDbwIndex: Compute the S_Dbw Validity Index for 'TitanCNA' model...
correctReadDepth: Correct GC content and mappability biases in sequencing data...
extractAlleleReadCounts: Function to extract allele read counts from a sequence...
loadDefaultParameters: Load TITAN parameters
runEMclonalCN: Function to run the Expectation Maximization Algorithm in...
TitanCNA-dataset: TITAN EM trained results for an example dataset
wigToRangedData: WIG Import Functions
See all...

All man pages Function index File listing

Man pages

computeSDbwIndex: Compute the S_Dbw Validity Index for 'TitanCNA' model...
correctReadDepth: Correct GC content and mappability biases in sequencing data...
extractAlleleReadCounts: Function to extract allele read counts from a sequence...
filterData: Filter list object based on read depth and missing data
getPositionOverlap: Function to assign values to given chromosome-position that...
loadAlleleCounts: Function to load tumour allele counts from a text file or...
loadDefaultParameters: Load TITAN parameters
removeEmptyClusters: Post-process TitanCNA results by removing clusters with...
runEMclonalCN: Function to run the Expectation Maximization Algorithm in...
TitanCNA-dataset: TITAN EM trained results for an example dataset
TitanCNA-output: Formatting and printing 'TitanCNA' results.
TitanCNA-package: TITAN: Subclonal copy number and LOH prediction whole genome...
TitanCNA-plotting: Plotting functions for 'TitanCNA' results.
viterbiClonalCN: Function to run the Viterbi algorithm for 'TitanCNA'.
wigToRangedData: WIG Import Functions

Functions

EMresults Man page
TitanCNA Man page
TitanCNA-dataset Man page
TitanCNA-package Man page
betabinomialpdflog Source code
betapdflog Source code
binomialpdflog Source code
clonalCNDerivativeNUpdateEqn Source code
clonalCNDerivativePloidyUpdateEqn Source code
clonalCNDerivativeSUpdateEqn Source code
clonalCNDerivativeVarExactUpdateEqn Source code
clonalCNDerivativeVarUpdateEqn Source code
clonalCNSVarUpdateEqn Source code
clonalNSUpdateEqn Source code
clonalTwoComponentMixtureCN Source code
computeBIC Source code
computeBinomialObslik Source code
computeNormalObslik Source code
computeSDbwIndex Man page Source code
convergeParams Man page
correctReadDepth Man page Source code
correctReadcount Source code
data Man page
decodeLOH Source code
decoupleMegaVar Source code
dirichletpdflog Source code
estimateBetaParamsMap Source code
estimateClonalCNParamsMap Source code
estimateClonalMixWeightsParamMap Source code
estimateDirichletParamsMap Source code
estimateGenotypeMixWeightsParamMap Source code
estimateInvGammaParamsMap Source code
excludeGarbageState Source code
extractAlleleReadCounts Man page Source code
filterData Man page Source code
getGenomeWidePositions Source code
getMajorMinorCN Source code
getPositionOverlap Man page Source code
getSubcloneProfiles Source code
invgammapdflog Source code
likelihoodFunc Source code
loadAlleleCounts Man page Source code
loadDefaultParameters Man page Source code
normalpdflog Source code
onLoad Source code
outlierObslik Source code
outputModelParameters Man page Source code
outputTitanResults Man page Source code
outputTitanSegments Man page Source code
plotAllelicCN Source code
plotAllelicRatio Man page Source code
plotCNlogRByChr Man page Source code
plotChrLines Source code
plotClonalFrequency Man page Source code
plotGeneAnnotation Source code
plotSegmentMedians Source code
plotSubcloneProfiles Man page Source code
printSDbw Source code
removeCentromere Source code
removeEmptyClusters Man page Source code
runEMclonalCN Man page Source code
sdbw.density Source code
setGenomeStyle Source code
setupClonalParameters Source code
updateParameters Source code
viterbiClonalCN Man page Source code
wigToRangedData Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/correction.R
R/hmmClonal.R
R/paramEstimation.R
R/plotting.R
R/utils.R
R/zzz.R
README
build
build/vignette.rds
data
data/EMresults.rda
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/TitanCNA.R
inst/doc/TitanCNA.Rnw
inst/doc/TitanCNA.pdf
inst/extdata
inst/extdata/gc_chr2.wig
inst/extdata/map_chr2.wig
inst/extdata/test_alleleCounts_chr2.txt
inst/extdata/test_norm_chr2.wig
inst/extdata/test_tum_chr2.wig
man
man/TitanCNA-dataset.Rd
man/TitanCNA-output.Rd
man/TitanCNA-package.Rd
man/TitanCNA-plotting.Rd
man/computeSDbwIndex.Rd
man/correctReadDepth.Rd
man/extractAlleleReadCounts.Rd
man/filterData.Rd
man/getPositionOverlap.Rd
man/loadAlleleCounts.Rd
man/loadDefaultParameters.Rd
man/removeEmptyClusters.Rd
man/runEMclonalCN.Rd
man/viterbiClonalCN.Rd
man/wigToRangedData.Rd
src
src/fwd_backC_clonalCN.c
src/getPositionOverlapC.c
src/register.c
src/titan.h
src/viterbiC_clonalCN.c
vignettes
vignettes/TitanCNA.Rnw
vignettes/TitanCNA.bib
TitanCNA documentation built on May 20, 2017, 9:58 p.m.

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