Performs SC3 clustering on matrix slot — perform.sc3.slot.cluster • IBRAP

Performs SC3 clustering on defined method-assays slot.

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

Arguments

object: IBRAP S4 class object
assay: Character. String containing indicating which assay to use
slot: Character. Which slot within the assay should be supplied.
HVGs: Boolean. Should previously the count matrix be subset to highly variable genes.
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.

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