# Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

## Documentation for package ‘mitoClone2’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
exclusionlists | Mitochondrial exclusionlist
getAlleleCount | mutationCalls counts accessor
getCloneLikelihood | mutationCalls accessors
getConfidence | mutationCalls accessors
getMainClone | mutationCalls accessors
getMut2Clone | mutationCalls accessors
getVarsCandidate | mutationCalls cluster accessor
mitoPlot | Plot clone-specific variants in circular plots
mut2GR | Convert mutation string to GRanges
mutationCalls | mutationCalls class
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
M_P1 | Mitochondrial exclusionlist
M_P2 | Mitochondrial exclusionlist
N_P1 | Mitochondrial exclusionlist
N_P2 | Mitochondrial exclusionlist
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