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

## Documentation for package ‘TitanCNA’ version 1.25.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'.
wigToGRanges | WIG Import Functions. wigToGRanges (new) and wigToRangedData (deprecated)
wigToRangedData | WIG Import Functions. wigToGRanges (new) and wigToRangedData (deprecated)