TitanCNA-dataset        TITAN EM trained results for an example dataset
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
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'.
viterbiClonalCN         Function to run the Viterbi algorithm for
                        'TitanCNA'.
wigToRangedData         WIG Import Functions. wigToGRanges (new) and
                        wigToRangedData (deprecated)
