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

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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.

Author
Gavin Ha, Sohrab P Shah
Date of publication
None
Maintainer
Gavin Ha <gavinha@broadinstitute.org>, Sohrab P Shah <sshah@bccrc.ca>
License
GPL-3
Version
1.12.0
URLs

View on Bioconductor

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

Files in this package

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