bam2R_10x               Read nucleotide counts from a 10x Genomics .bam
                        file
baseCountsFromBamList   Create a list object from a list of single-cell
                        BAM files where each contains a matrix of the
                        of AGCT nt counts at chosen sites
clusterMetaclones       Cluster mutations into clones - following the
                        tree structure
data                    Mitochondrial exclusionlist
getAlleleCount          mutationCalls counts accessor
getCloneLikelihood      mutationCalls accessors
getVarsCandidate        mutationCalls cluster accessor
mitoPlot                Plot clone-specific variants in circular plots
mut2GR                  Convert mutation string to GRanges
mutationCalls-class     mutationCalls class
mutationCallsFromCohort
                        Create a mutationCalls objects from nucleotide
                        base calls and defines a exclusionlist (cohort)
mutationCallsFromExclusionlist
                        Create a mutationCalls object from nucleotide
                        base calls using a exclusionlist (single
                        individual)
mutationCallsFromMatrix
                        mutationCalls constructor
overwriteMetaclones     Manually overwrite clustering of mutations into
                        clones
plotClones              Plot clonal assignment of single cells
predictCellAssignment   Predict cell assignments from fitted Vireo
                        model
pullcountsVars          Pull variant counts
quick_cluster           Quick clustering of mutations
removeWindow            Remove mutations that occuring at the same site
setVarsCandidate        mutationCalls cluster setter
varCluster              Inference of mutational trees by of single cell
                        mutational status
vireo                   Initialize Vireo model
vireoFit                Fit Vireo model with multiple initializations
