create_seurat_object_default: Create Seurat object

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

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 Seurat package (default parameters).
umap_embedding	The UMAP embedding of the expression matrix. If NULL, the umap will be created using the Seurat package (default parameters).
metadata_df	The metadata dataframe having the cell names as rownames. If NULL, a dataframe with a single column named identical_ident will be created.

Value

A Seurat object of the expression matrix, having the stable number of clusters identified by ClustAssess.

Core-Bioinformatics/ClustAssess documentation built on Nov. 4, 2024, 1:05 p.m.