clusterMetaclones: Cluster mutations into clones - following the tree structure

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Cluster mutations into clones - following the tree structure

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 = TRUE)

Arguments

mutcalls	mutcalls object of class mutationCalls for which varCluster 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.

Value

Returns the provided mutationCalls class object with an additional 'mainClone' metadata which allows for further refinement of clonal population and association of cells with a cluster of mutations (in this case clones).

Examples

P1 <- readRDS(system.file("extdata/sample_example1.RDS",package = "mitoClone2"))
P1 <- clusterMetaclones(P1)
## access via mainClone metadata

benstory/mitoClone2 documentation built on Oct. 30, 2024, 3:20 p.m.