run_kmeans_clustering: Run k-means clustering for a specific 'k'.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Run k-means clustering for a specific k.

Description

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.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.