Run Azimuth annotation for ATAC query

# S3 method for Seurat
RunAzimuthATAC(
  query,
  reference,
  fragment.path = NULL,
  annotation.levels = NULL,
  umap.name = "ref.umap",
  verbose = TRUE,
  assay = NULL,
  k.weight = 50,
  n.trees = 20,
  mapping.score.k = 100,
  dims.atac = 2:50,
  dims.rna = 1:50
)

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

RunAzimuthATAC(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 ext.Rds

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

assay

query assay name

dims.atac

dimensions

dims.rna

dimensions

do.adt

transfer ADT assay

Value

Seurat object with reference reductions and annotations

Returns a Seurat object containing celltype annotations