runKmeans: runKmeans

In JhuangLab/flowSpy: A Toolkit for Flow And Mass Cytometry Data

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 FSPY 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 FSPY object with kmeans.id in meta.data

See Also

kmeans

Examples

if (FALSE) {
fspy <- runKmeans(fspy, k = 25, verbose = TRUE)
}

JhuangLab/flowSpy documentation built on July 15, 2020, 8:31 a.m.