perform.sc3.reduction.cluster: Performs SC3 clustering on reduced embeddings

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

Performs SC3 clustering on reduced embeddings

Description

Performs SC3 clustering on defined method-assays and supplied reductions. SC3 is designed to function on count matrices, reduction may not always work well.

Usage

perform.sc3.reduction.cluster(
  object,
  assay,
  reduction,
  dims,
  cluster.df.name.suffix = "",
  ks,
  n.core = 3
)

Arguments

object	IBRAP S4 class object
assay	Character. String containing indicating which assay to use
reduction	Character. String defining which reduction to supply to the clustering algorithm.
dims	Numerical. How many dimensions of the reduciton should be supplied, NULL equates to all.
ks	Numerical range. Number of clusters to identify, this can be a range, i.e. 5:10.
n.core	Numerical. How many cores should be used to run SC3. Default = 3
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.