Run scGate — RunScGate • RIRA

Helper function to run scGate

Usage

RunScGate(
  seuratObj,
  model,
  min.cells = 30,
  assay = "RNA",
  pos.thr = 0.13,
  neg.thr = 0.13,
  ncores = 1,
  output.col.name = "is.pure",
  genes.blacklist = "default",
  doPlotUCellScores = TRUE
)

Arguments

seuratObj: The seurat object
model: Either an scGate model, or a character that will be passed to GetScGateModel()
min.cells: Passed directly to scGate::scGate. Stop iterating if fewer than this number of cells is left
assay: Passed directly to scGate::scGate. Seurat assay to use
pos.thr: Passed directly to scGate::scGate. Minimum UCell score value for positive signatures
neg.thr: Passed directly to scGate::scGate. Maximum UCell score value for negative signatures
ncores: Passed directly to scGate::scGate. Number of processors for parallel processing (requires future.apply)
output.col.name: Passed directly to scGate::scGate. Column name with 'pure/impure' annotation
genes.blacklist: Passed directly to scGate::scGate. Genes blacklisted from variable features. The default loads the list of genes in scGate::genes.blacklist.default; you may deactivate blacklisting by setting genes.blacklist=NULL
doPlotUCellScores: If true, FeaturePlots will be created for each UCell score used in classification