perform.reduction.kmeans: Performs Kmeans/PAM clustering on a reduction

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Performs Kmeans/PAM clustering on a reduction

Description

Performs Kmeans/PAM clustering on defined method-assays a defined reduction.

Usage

perform.reduction.kmeans(
  object,
  assay,
  reduction = NULL,
  dims = NULL,
  k = NULL,
  cluster.df.name.suffix = "",
  method = "kmeans",
  ...
)

Arguments

object	IBRAP S4 class object
assay	Character. String containing indicating which assay to use
reduction	Character. Which reduction(s) within the assay should be supplied. Default = NULL
dims	Numerical. How many dimensions of the reduction should be supplied.Default = NULL
k	Numerical. How many clusters should the algorithm identify, this can be a range. Default = NULL
method	Which algorithm should be used, options: 'kmeans', 'pam'. Default = 'kmeans
...	Arguments to be passed to either base::kmeans or cluster::pam, depending on the defined method
assignment.df.name	Character. What to call the df contained in clusters.

Value

Cluster assignments using the list of resolutions provided contained within cluster_assignments under assignment.df.name

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.