Skip to contents

Classify T/NK

Classify_Myeloid.Rd

Runs celltypist using the RIRA Myeloid model to score cells using CellTypist with optimized parameters.

Usage

Classify_Myeloid(
  seuratObj,
  assayName = Seurat::DefaultAssay(seuratObj),
  columnPrefix = "RIRA_Myeloid_v3.",
  maxAllowableClasses = 6,
  minFractionToInclude = 0.01,
  minCellsToRun = 200,
  maxBatchSize = 6e+05,
  retainProbabilityMatrix = FALSE
)

Arguments

seuratObj

The seurat object

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