RunCellTypist: Run Celltypist

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

Run Celltypist

Description

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 [e-mail]
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.

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