setBrayClusters: Set Bray clusters

In SingerLab/gac: Genetic Analysis of Cells

Set Bray clusters

Description

Set Bray clusters

Usage

setBrayClusters(
  cnr,
  tree.height = NULL,
  prefix = "C",
  opt.method = "maxp",
  ...
)

Arguments

cnr	a cnr bundle
tree.height	height of the tree optClust
prefix	a prefix to append before the cluster number
opt.method	optimization method, must be either "mi" or 'maxp' ; default is 'mi'
...	additional parameters passed to optClust

Value

Returns a cnr object with cluster membership based on Bray-Curtis Ward.D2 heirarchical clustering. If method is "mi" the the tree height is calculated using minimum.intersect. Where optimal height is the value at the intersect between the number of one-cell and multi-cell clusters. If method is "maxp",

Examples

data(cnr)
noisy.cells <- cnr$qc$cellID[cnr$qc$qc.status == "FAIL"]
cnr <- excludeCells(cnr, excl = noisy.cells)

cnr <- phylo_cnr(cnr, root.cell = "cell0")

cnr <- setBrayClusters(cnr)

cnr <- setBrayClusters(cnr, opt.method = "maxp")

cnr <- setBrayClusters(cnr, tree.height = 0.16)

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.