run_consensus_clustering: run consensus clustering

View source: R/run_consensus_clustering.R

run_consensus_clusteringR Documentation

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.