RunScGateWithRhesusModels: Run scGate using Rhesus macaque models

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

Run scGate using Rhesus macaque models

Description

Helper function to run scGate, iterating the provided models and generating a consensus field

Usage

RunScGateWithRhesusModels(
  seuratObj,
  min.cells = 30,
  assay = "RNA",
  pos.thr = 0.13,
  neg.thr = 0.13,
  ncores = 1,
  genes.blacklist = "default",
  dropAmbiguousConsensusValues = FALSE
)

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
dropAmbiguousConsensusValues	If true, any consensus calls that are ambiguous will be set to NA

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