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

View source: R/phyloCNR.R

phyloDDRCR Documentation

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.