runKmeans {CytoTree}R Documentation

runKmeans

Description

Perform k-means clustering on a data matrix.

Usage

runKmeans(
  object,
  k = 25,
  iter.max = 10,
  nstart = 1,
  algorithm = c("Hartigan-Wong", "Lloyd", "Forgy", "MacQueen"),
  trace = FALSE,
  scale = FALSE,
  verbose = FALSE,
  ...
)

Arguments

object

an CYT object

k

numeric. The number of clusters.

iter.max

numeric. The maximum number of iterations allowed.

nstart

numeric. If k is a number, how many random sets should be chosen.

algorithm

character. Type of algorithm that will be choosen to calculate kmeans. Four algoritms are provided: Hartigan-Wong, Lloyd, Forgy, MacQueen.

trace

logical or integer number.

scale

logical. Whether to use scaled data in kmeans.

verbose

logical. Whether to print calculation progress.

...

Parameters passing to kmeans function

Value

an CYT object with kmeans.id in meta.data

See Also

kmeans

Examples


cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- runKmeans(cyt, k = 25, verbose = TRUE)
[Package CytoTree version 1.2.0 Index]