runPhylo: Run phylogenetic analysis

In navinlabcode/copykit: CopyKit

Run phylogenetic analysis

Description

Performs phylogenetic analysis

Usage

runPhylo(
  scCNA,
  method = "nj",
  metric = "euclidean",
  assay = "segment_ratios",
  n_threads = parallel::detectCores()/4
)

Arguments

scCNA	scCNA object.
method	Phylogenetic method to be run, currently accepts "nj" (neighbor-joining) and "me" (minimum evolution). Defaults to "nj".
metric	distance metric passed to construct the phylogeny (Defaults to "euclidean").
assay	String with the name of the assay to pull data from to run phylogenetic analysis. Note that only assay named "integer" will be treated as integer.
n_threads	Number of threads used to calculate the distance matrix. Passed to 'amap::Dist'

Value

A rooted phylogenetic tree object in the slot phylo from scCNA object. Access phylo slot with: copykit::phylo(scCNA)

Author(s)

Darlan Conterno Minussi

Junke Wang

Examples

set.seed(1000)
copykit_obj <- copykit_example_filtered()[,sample(50)]
copykit_obj <- runPhylo(copykit_obj)

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