computeSDbwIndex        Compute the S_Dbw Validity Index for 'TitanCNA'
                        model selection
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
filterData              Filter list object based on read depth and
                        missing data and returns a filtered data.table
                        object.
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.
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')
outputTitanResults      Formatting and printing 'TitanCNA' results.
plotCNlogRByChr         Plotting functions for 'TitanCNA' results.
runEMclonalCN           Function to run the Expectation Maximization
                        Algorithm in 'TitanCNA'.
TitanCNA-dataset        TITAN EM trained results for an example dataset
TitanCNA-package        TITAN: Subclonal copy number and LOH prediction
                        whole genome sequencing of tumours
viterbiClonalCN         Function to run the Viterbi algorithm for
                        'TitanCNA'.
wigToRangedData         WIG Import Functions. wigToGRanges (new) and
                        wigToRangedData (deprecated)
