Convert single cell experiment to Seurat
Usage
# S3 method for class 'cell_data_set'
as.Seurat(
x,
counts = "counts",
data = NULL,
assay = "RNA",
project = "cell_data_set",
loadings = NULL,
clusters = NULL,
...
)
Details
The cell_data_set
method for as.Seurat
utilizes the SingleCellExperiment
method of
as.Seurat
to handle moving over expression data, cell
embeddings, and cell-level metadata. The following additional information
will also be transfered over:
Feature loadings from
cds@reduce_dim_aux$gene_loadings
will be added to the dimensional reduction specified byloadings
or the name of the first dimensional reduction that contains "pca" (case-insensitive) ifloadings
is not setMonocle 3 clustering will be set as the default identity class. In addition, the Monocle 3 clustering will be added to cell-level metadata as “monocle3_clusters”, if present
Monocle 3 partitions will be added to cell-level metadata as “monocle3_partitions”, if present
Monocle 3 pseudotime calculations will be added to “monocle3_pseudotime”, if present
The nearest-neighbor graph, if present, will be converted to a
Graph
object, and stored as “assay
_monocle3_graph”