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

Description Usage Arguments Value

View source: R/phyloCNR.R

Description

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

Usage

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

Arguments

cnr

a cnr bundle

exclude.clones

vector of clones to exclude

root.clone

a single clone to root the tree

dist.method

method for calculating cell-to-cell distance (see vegan::vegdist)

hclust.method

method for heirarchical clustering (see hclust)

...

other parameters

Value

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


SingerLab/gac documentation built on Aug. 14, 2021, 10:57 a.m.