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

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Documentation for package ‘mitoClone2’ version 1.12.0

• 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
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