create_seurat_object_from_clustassess_app: Create Seurat object from a ClustAssess shiny app

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Create Seurat object from a ClustAssess shiny app

Description

Use the files generated in the ClustAssess app to create a Seurat object which has the stable number of clusters.

Usage

create_seurat_object_from_clustassess_app(
  app_folder,
  stable_feature_type,
  stable_feature_set_size,
  stable_clustering_method,
  stable_n_clusters = NULL,
  use_all_genes = FALSE
)

Arguments

app_folder	Path pointing to the folder containing a ClustAssess app.
stable_feature_type	The feature type which leads to stable clusters.
stable_feature_set_size	The feature size which leads to stable clusters.
stable_clustering_method	The clustering method which leads to stable clusters.
stable_n_clusters	The number of clusters that are stable. If NULL, all the clusters will be provided. Defaults to NULL.
use_all_genes	A boolean value indicating if the expression matrix should be truncated to the genes used in the stability assessment. Defaults to FALSE.

Value

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

Core-Bioinformatics/ClustAssess documentation built on Nov. 14, 2024, 6:33 p.m.