RunScGateForModels: Run scGate for 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 for models

Description

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

Usage

RunScGateForModels(
  seuratObj,
  modelNames,
  min.cells = 30,
  assay = "RNA",
  pos.thr = 0.13,
  neg.thr = 0.13,
  ncores = 1,
  genes.blacklist = "default",
  labelRename = NULL,
  dropAmbiguousConsensusValues = FALSE,
  consensusModels = NULL
)

Arguments

seuratObj	The seurat object
modelNames	A vector of model names to run. They are assumed to be non-overlapping populations
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
consensusModels	An optional list of model names to consider for the consensus call. This allows many models to be run, yet only consider a subset when creating the consensus call. This might be useful if some models overlap or produce false-positives.

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