RunScGate: Run scGate

In bimberlabinternal/RIRA_classification: A package for the Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells

Run scGate

Description

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

bimberlabinternal/RIRA_classification documentation built on April 14, 2025, 5:59 p.m.