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
correctReadDepth        Correct GC content and mappability biases in
                        sequencing data read counts
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
outputTitanResults      Formatting and printing 'TitanCNA' results.
plotCNlogRByChr         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'.
viterbiClonalCN         Function to run the Viterbi algorithm for
                        'TitanCNA'.
wigToRangedData         WIG Import Functions
