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Run Celltypist

RunCellTypist.Rd

Runs celltypist on a seurat object and stores the calls as metadata

Usage

RunCellTypist(
  seuratObj,
  modelName = "Immune_All_Low.pkl",
  pThreshold = 0.5,
  minProp = 0,
  useMajorityVoting = TRUE,
  mode = "prob_match",
  extraArgs = c("--mode", mode, "--p-thres", pThreshold, "--min-prop", minProp),
  assayName = Seurat::DefaultAssay(seuratObj),
  columnPrefix = NULL,
  maxAllowableClasses = 6,
  minFractionToInclude = 0.01,
  minCellsToRun = 200,
  maxBatchSize = 1e+05,
  retainProbabilityMatrix = FALSE,
  runCelltypistUpdate = TRUE
)

Arguments

seuratObj

The seurat object

modelName

The model name or path to celltypist model

pThreshold

By default, this would be passed to the –p-thres argument. However, if you also provide extraArgs, this is ignored.

minProp

By default, this would be passed to the –min-prop argument. However, if you also provide extraArgs, this is ignored.

useMajorityVoting

If true, the celltypist –majority-voting option will be added.

mode

Passed directly to the celltypist –mode argument. Either best_match or prob_match

extraArgs

An optional list of additional arguments passed directly on the command line to cell typist

assayName

The name of the assay to use. Others will be dropped

columnPrefix

A prefix that will be added to the beginning of the resulting columns, added the seurat@meta.data

maxAllowableClasses

Celltypist can assign a cell to many classes, creating extremely long labels. Any cell with more than this number of labels will be set to NA

minFractionToInclude

If non-null, any labels with fewer than this fraction of cells will be set to NA.

minCellsToRun

If the input seurat object has fewer than this many cells, NAs will be added for all expected columns and celltypist will not be run.

maxBatchSize

If more than this many cells are in the object, it will be split into batches of this size and run in serial.

retainProbabilityMatrix

If true, the celltypist probability_matrix with per-class probabilities will be stored in meta.data

runCelltypistUpdate

If true, –update-models will be run for celltypist prior to scoring cells.