runClara {CytoTree}R Documentation

runClara

Description

Clustering a data matrix into k clusters

Usage

runClara(
  object,
  k = 25,
  metric = c("euclidean", "manhattan", "jaccard"),
  stand = FALSE,
  samples = 5,
  scale = TRUE,
  trace = 0,
  verbose = FALSE,
  ...
)

Arguments

object

a CYT object

k

numeric. The number of clusters. It is required that 0 < k < n where n is the number of observations (i.e., n = nrow(x)).

metric

character. string specifying the metric to be used for calculating dissimilarities between observations.

stand

logical. Indicating if the measurements in x are standardized before calculating the dissimilarities.

samples

numeric. Say N, the number of samples to be drawn from the dataset. The default is N = 5,

scale

logical. Whether to use scaled data in kmeans.

trace

numberic. Indicating a trace level for diagnostic output during the algorithm

verbose

logical. Whether to print calculation progress.

...

Parameters passing to clara function

Value

a CYT object with clara.id in meta.data

See Also

clara

Examples


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

cyt <- runClara(cyt, k = 25, verbose = TRUE)



[Package CytoTree version 1.0.3 Index]