Run scGate for models

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.