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


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Documentation for package ‘mitoClone2’ version 1.0.0

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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