perform.sc3.slot.cluster: Performs SC3 clustering on matrix slot

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

Performs SC3 clustering on matrix slot

Description

Performs SC3 clustering on defined method-assays slot.

Usage

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.

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.