RunAzimuth.Seurat | R Documentation |
Run Azimuth annotation
## S3 method for class '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 class 'character'
RunAzimuth(query, ...)
RunAzimuth(query, ...)
query |
Seurat object or following type of path:
|
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 |
Seurat object with reference reductions and annotations
Returns a Seurat object containing celltype annotations
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