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
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
