mutationCalls class

Description

To create this class from a list of bam files (where each bam file corresponds to a single cell), use mutationCallsFromCohort or mutationCallsFromExclusionlist. To create this class if you already have the matrices of mutation counts, use its contstructor, i.e. mutationCallsFromMatrix(M = data1, N = data2).

Slots

M

A matrix of read counts mapping to the mutant allele. Columns are genomic sites and rows and single cells.

N

A matrix of read counts mapping to the nonmutant alleles. Columns are genomic sites and rows and single cells.

ternary

Discretized version describing the mutational status of each gene in each cell, where 1 signfiies mutant, 0 signifies reference, and ? signifies dropout

cluster

Boolean vector of length ncol(M) specifying if the given mutation should be included for clustering (TRUE) or only used for annotation.

metadata

Metadata frame for annotation of single cells (used for plotting). Row names should be the same as in M

tree

Inferred mutation tree

cell2clone

Probability matrix of single cells and their assignment to clones.

mut2clone

Maps mutations to main clones

mainClone

Probability matrix of single cells and their assignment to main clones

treeLikelihoods

Likelihood matrix underlying the inference of main clones, see clusterMetaclones