RunScGateWithDefaultModels: Run scGate With DefaultModels

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

Run scGate With DefaultModels

Description

Helper function to run scGate, running all human models in scGate::get_sc()

Usage

RunScGateWithDefaultModels(
  seuratObj,
  min.cells = 30,
  assay = "RNA",
  pos.thr = 0.13,
  neg.thr = 0.13,
  ncores = 1,
  genes.blacklist = "default",
  labelRename = NULL,
  dropAmbiguousConsensusValues = FALSE,
  excludedModels = c("Male", "Female")
)

Arguments

seuratObj	The seurat object
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)
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
labelRename	An optional list that maps the model name to the final label that should be used in the seurat object. for exmaple: list(Tcell = 'T_NK', NK = 'T_NK'), would re-label cells classified as either 'Tcell' or 'NK' by those models to one common label of T_NK
dropAmbiguousConsensusValues	If true, any consensus calls that are ambiguous will be set to NA
excludedModels	An optional vector of model names to exclude

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