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

## Documentation for package ‘TitanCNA’ version 1.14.0

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

## 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
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
extractAlleleReadCounts | Function to extract allele read counts from a sequence alignment (BAM) file
filterData | Filter list object based on read depth and missing data
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
loadDefaultParameters | Load TITAN parameters
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.
plotSubcloneProfiles | Plotting functions for 'TitanCNA' results.
removeEmptyClusters | Post-process TitanCNA results by removing clusters with proportion of data points altered lower than a threshold. The number of clonal clusters, cellular prevalence, and normal contamination will be adjusted to reflect the remaining clonal clusters.
runEMclonalCN | Function to run the Expectation Maximization Algorithm in 'TitanCNA'.
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