phyloDDRC: Calculating clone-to-clone distances, and estimating a...

In SingerLab/gac: Genetic Analysis of Cells

Calculating clone-to-clone distances, and estimating a phylogenetic tree

Description

Calculating clone-to-clone distances, and estimating a phylogenetic tree

Usage

phyloDDRC(
  cnr,
  root.clone = NULL,
  exclude.clones = NULL,
  dist.method = "bray",
  hclust.method = "ward.D2",
  ...
)

Arguments

cnr	a cnr bundle
root.clone	a single clone to root the tree
exclude.clones	vector of clones to exclude
dist.method	method for calculating cell-to-cell distance (see vegan::vegdist)
hclust.method	method for heirarchical clustering (see hclust)
...	other parameters passed to vegan

Value

Creates a cell-to-cell distance matrix, runs heirarchical clustering, and converts the 'hclust' object to an 'ape' class 'phylo' object.

• cdb cell to cell Bray-Curtis dissimiarly

• hcdb heirarchical clustering of distance matrix

• phylo ape class 'phylo' object

SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.