runConsensusPhylo: runConsensusPhylo

In navinlabcode/copykit: CopyKit

runConsensusPhylo

Description

Runs a minimal evolution tree algorithm for the consensus data frame

Usage

runConsensusPhylo(scCNA, root = c("mrca", "neutral", "user"), root_user = NULL)

Arguments

scCNA	The scCNA object.
root	A string indicating how to root the consensus tree.
root_user	A numeric with the vector to be used as root of the tree if root is set to 'user'. Must have the same length as the number of bins of the genome scaffold.

Value

A phylo object with a consensus tree stored in the consensusPhylo slot of the CopyKit object.

Examples

copykit_obj <- copykit_example_filtered()
copykit_obj <- findClusters(copykit_obj)
copykit_obj <- calcConsensus(copykit_obj)
copykit_obj <- runConsensusPhylo(copykit_obj)
plotPhylo(copykit_obj, consensus = TRUE, label = "subclones")

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.