Run k-means clustering for a specific k.

Run k-means clustering for a specific k.

Usage

run_kmeans_clustering(
  sce,
  kmeans_k,
  is_integration,
  dimred = "pca",
  nstart = 25,
  iter.max = 1000
)

Arguments

sce

A SingleCellExperiment object.

kmeans_k

An integer scalar: number of clusters for k-means.

is_integration

A logical scalar: if TRUE, clusterings will be named as cluster_int_*, otherwise cluster_*.

dimred

A character scalar: name of matrix in reducedDim() used for k-means.

nstart, iter.max

Passed to stats::kmeans().

Value

A tibble whose columns are mostly self-explanatory, except the data column, which is of list type and contains an another tibble with kmeans_object column holding an object of class kmeans returned from the stats::kmeans() function.