Run Azimuth annotation

Source: R/azimuth.R, R/generics.R

Run Azimuth annotation

# S3 method for Seurat
RunAzimuth(
  query,
  reference,
  query.modality = "RNA",
  annotation.levels = NULL,
  umap.name = "ref.umap",
  do.adt = FALSE,
  verbose = TRUE,
  assay = NULL,
  k.weight = 50,
  n.trees = 20,
  mapping.score.k = 100,
  ...
)

# S3 method for character
RunAzimuth(query, ...)

RunAzimuth(query, ...)

Arguments

query

Seurat object or following type of path:

  • A .h5 matrix

  • A .rds file containing a Seurat object

  • A .h5ad anndata object

  • A .h5seurat object

reference

Name of reference to map to or a path to a directory containing ref.Rds and idx.annoy

annotation.levels

list of annotation levels to map. If not specified, all will be mapped.

umap.name

name of umap reduction in the returned object

do.adt

transfer ADT assay

assay

query assay name

Value

Seurat object with reference reductions and annotations

Returns a Seurat object containing celltype annotations