run_consensus_clustering: run consensus clustering

In SingerLab/gac: Genetic Analysis of Cells

run consensus clustering

Description

Function runs consensus clustering for a pre-determined sequence of K.

Usage

run_consensus_clustering(
  cnr,
  maxK = 40,
  iters = 200,
  title = "cnr_ccp",
  innerLinkage = "ward.D2",
  finalLinkage = "ward.D2",
  seed = 2020.0314,
  verbose = TRUE,
  ...
)

Arguments

cnr	a cnr object
maxK	maximum K, end of K sequence
iters	number of times the clustering runs
title	title for the consensus cluster map
innerLinkage	inner linkage, see ConsensusClusterPlus
finalLinkage	final linkage, see ConsensusClusterPlus
seed	seed of analysis
verbose	print out progress
...	additional parameters for ConsensusClusterPlus e.g. plot = "png"

Value

A cnr object that contains the output of ConsensusClusterPlus for the specified Ks.

• ccp ConsensusClusterPlus object

Examples

data(cnr)

cnr <- phyloCNR(cnr)

cnr <- run_consensus_clustering(cnr, maxK = 6)

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