annotate_celltypes: Annotate normal human and mouse cells in seurat object.

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Annotate normal human and mouse cells in seurat object.

Description

If specifying "species" argument, both human and mouse cell reference are built by combining individual normal cell and immune celldex references.

Usage

annotate_celltypes(
  sobject,
  species = "",
  ref,
  labels,
  aggr_ref = FALSE,
  label_type = "label.main",
  ...
)

Arguments

sobject	A seurat object that you would like to annotate
species	Takes "human" or "mouse" as a built in. Overrides ref and labels if set
ref	Reference passed to Singler. Either a single or a list of multiple
labels	Reference labels passed to SingleR. Either a single or a list of multiple
aggr_ref	Passed to SingleR to control aggregation of the references prior to annotation, see trainSingleR.
label_type	Either "label.main", "label.fine" or "label.ont" if using species argument. Not needed otherwise
...	Other options passed to SingleR

Value

A seurat object with cell_type and cell_scores added to metadata

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.