Subclonal copy number and LOH prediction whole genome sequencing of tumours

Documentation for package ‘TitanCNA’ version 1.0.0

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
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
loadAlleleCountsFromFile	Function to load tumour allele counts from a text file
loadDefaultParameters	Load TITAN parameters
outputModelParameters	Formatting and printing 'TitanCNA' results.
outputTitanResults	Formatting and printing 'TitanCNA' results.
plotAllelicRatio	Plotting functions for 'TitanCNA' results.
plotClonalFrequency	Plotting functions for 'TitanCNA' results.
plotCNlogRByChr	Plotting functions for 'TitanCNA' results.
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'.