overwriteMetaclones: Manually overwrite clustering of mutations into clones

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

Manually overwrite clustering of mutations into clones

Description

The function clusterMetaclones provides an automated way to group mutations into clones for subsequent analyses (such as differential expression analyses). In practice, it may make sense to overwrite these results manually. See the vignette 'Computation of clonal hierarchies and clustering of mutations' for an example.

Usage

overwriteMetaclones(mutcalls, mutation2clones)

Arguments

mutcalls	mutcalls object of class mutationCalls for which clusterMetaclones has been run
mutation2clones	Named integer vector that assigns mutations to clones. See the vignette 'Computation of clonal hierarchies and clustering of mutations' for an example.

Value

Returns the provided mutationCalls class object with the 'mainClone' metadata overwritten with the manual values provided by the user.

Examples

P1 <- readRDS(system.file("extdata/sample_example1.RDS",package = "mitoClone2"))
new.n <- seq(17)
names(new.n) <- names(getMut2Clone(P1))
P1.newid <- overwriteMetaclones(P1,new.n)

benstory/mitoClone2 documentation built on Nov. 8, 2023, 12:13 a.m.