Performs SC3 clustering on reduced embeddings — perform.sc3.reduction.cluster • IBRAP

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

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