clusterMetaclones: Cluster mutations into clones - following the tree structure

In veltenlab/mitoClone: Clonal tracking in single-cell RNA-seq data using mitochondrial and somatic mutations

Description

PhISCS orders all mutations into a hierarchical mutational tree; in many cases, the exact order of the acquisition of individual mutations in not unanimously determined from the data. This function computes the change in likelihood of the infered clonal assignment if two mutations are merged into a clone. Hierarchical clustering is then used to determine the clonal structure. The result is visualized and should be fine-tuned using the min.lik parameter.

Usage

clusterMetaclones(mutcalls, min.lik = 1, plot = T)

Arguments

mutcalls	mutcalls object of class mutationCalls for which muta_cluster has been run
min.lik	specifies the minimum difference in likelihood required. This parameter is set arbitrarily, see the vignette "Computation of clonal hierarchies and clustering of mutations" for more information.
plot	whether dendrograms should be plotted.

veltenlab/mitoClone documentation built on April 18, 2021, 5:19 a.m.