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

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Documentation for package ‘TitanCNA’ version 1.19.1

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TitanCNA-package TITAN: Subclonal copy number and LOH prediction whole genome sequencing of tumours
computeSDbwIndex Compute the S_Dbw Validity Index for 'TitanCNA' model selection
convergeParams TITAN EM trained results for an example dataset
correctIntegerCN Compute purity and ploidy corrected log ratios; recompute integer CN for high-level amplifications.
correctReadDepth Correct GC content and mappability biases in sequencing data read counts
data TITAN EM trained results for an example dataset
EMresults TITAN EM trained results for an example dataset
filterData Filter list object based on read depth and missing data and returns a filtered data.table object.
getHaplotypesFromVCF Function to load tumour allele counts from a text file or data.frame and returns a data.table ('loadHaplotypeAlleleCounts'). Function to load phased heterozygous sites from a VCF file ('getHaplotypesFromVCF')
getPositionOverlap Function to assign values to given chromosome-position that overlaps a list of chromosomal segments
loadAlleleCounts Function to load tumour allele counts from a text file or data.frame and returns a data.table.
loadBXcountsFromBEDDir Function to load tumour allele counts from a text file or data.frame and returns a data.table ('loadHaplotypeAlleleCounts'). Function to load phased heterozygous sites from a VCF file ('getHaplotypesFromVCF')
loadDefaultParameters Load TITAN parameters
loadHaplotypeAlleleCounts Function to load tumour allele counts from a text file or data.frame and returns a data.table ('loadHaplotypeAlleleCounts'). Function to load phased heterozygous sites from a VCF file ('getHaplotypesFromVCF')
outputModelParameters Formatting and printing 'TitanCNA' results.
outputTitanResults Formatting and printing 'TitanCNA' results.
outputTitanSegments Formatting and printing 'TitanCNA' results.
plotAllelicRatio Plotting functions for 'TitanCNA' results.
plotClonalFrequency Plotting functions for 'TitanCNA' results.
plotCNlogRByChr Plotting functions for 'TitanCNA' results.
plotHaplotypeFraction Plotting functions for 'TitanCNA' results.
plotSegmentMedians Plotting functions for 'TitanCNA' results.
plotSubcloneProfiles Plotting functions for 'TitanCNA' results.
runEMclonalCN Function to run the Expectation Maximization Algorithm in 'TitanCNA'.
setGenomeStyle Function to load tumour allele counts from a text file or data.frame and returns a data.table.
TitanCNA TITAN: Subclonal copy number and LOH prediction whole genome sequencing of tumours
TitanCNA-dataset TITAN EM trained results for an example dataset
viterbiClonalCN Function to run the Viterbi algorithm for 'TitanCNA'.
wigToRangedData WIG Import Functions