create_seurat_object_default {ClustAssess} | R Documentation |
Create Seurat object
Description
Use a normalized expression matrix and, potentially, an already generated PCA / UMAP embedding, to create a Seurat object.
Usage
create_seurat_object_default(
normalized_expression_matrix,
count_matrix = NULL,
pca_embedding = NULL,
umap_embedding = NULL,
metadata_df = NULL
)
Arguments
normalized_expression_matrix |
The normalized expression matrix having genes on rows and cells on columns. |
count_matrix |
The count matrix having genes on rows and cells on columns. If NULL, the normalized_expression_matrix will be used. |
pca_embedding |
The PCA embedding of the expression matrix. If NULL, the
pca will be created using the |
umap_embedding |
The UMAP embedding of the expression matrix. If NULL, the
umap will be created using the |
metadata_df |
The metadata dataframe having the cell names as rownames.
If NULL, a dataframe with a single column named |
Value
A Seurat object of the expression matrix, having the stable number of clusters identified by ClustAssess.