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

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
Date of publicationNone
MaintainerGavin Ha <gavinha@broadinstitute.org>, Sohrab P Shah <sshah@bccrc.ca>
LicenseGPL-3
Version1.12.0
https://github.com/gavinha/TitanCNA

View on Bioconductor

Functions

computeSDbwIndex Man page
convergeParams Man page
correctReadDepth Man page
data Man page
EMresults Man page
extractAlleleReadCounts Man page
filterData Man page
getPositionOverlap Man page
loadAlleleCounts Man page
loadDefaultParameters Man page
outputModelParameters Man page
outputTitanResults Man page
plotAllelicRatio Man page
plotClonalFrequency Man page
plotCNlogRByChr Man page
plotSubcloneProfiles Man page
removeEmptyClusters Man page
runEMclonalCN Man page
TitanCNA Man page
TitanCNA-dataset Man page
TitanCNA-package Man page
viterbiClonalCN Man page
wigToRangedData Man page

Files

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

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