fcluster: Cluster features

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Cluster features

Description

Cluster features

Usage

fcluster(
  object,
  distmat = NULL,
  method = "cmeans",
  k = 2:10,
  verbose = TRUE,
  plot = TRUE,
  label = if ("gene" %in% fvars(object)) "gene" else "feature_id",
  alpha = 1,
  nrow = if (length(method) > 1) length(method) else NULL,
  ncol = NULL
)

Arguments

object	SummarizedExperiment
distmat	distance matrix
method	'cmeans'
k	number of clusters
verbose	TRUE or FALSE
plot	TRUE or FALSE
label	fvar
alpha	fraction
nrow	number
ncol	number

Value

SummarizedExperiment

SummarizedExperiment

Examples

object <- twofactor_sumexp()
distmat <- fdist(object)
fcluster(object)                                                   # membership-based colors
fcluster(object, distmat)                                          # silhouette-based colors
fcluster(object, distmat, method = c('cmeans', 'hclust', 'pamk'))  # more methods

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.