Create monocle object from a ClustAssess shiny app

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

Usage

create_monocle_from_clustassess_app(
  app_folder,
  stable_feature_type,
  stable_feature_set_size,
  stable_clustering_method,
  stable_n_clusters = NULL,
  use_all_genes = FALSE,
  nrows_chunk = 1000,
  refresh_interval = 1
)

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.

nrows_chunk

The size of the chunk (in number of rows) to read from the expression.h5 file to form the sparse matrix. Defaults to 1000.

refresh_interval

The periodicity of chunks reading prior to running the garbage collector. Defaults to 1 iteration.

Value

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