write_objects: Write the objects for the ClustAssess ShinyApp

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Write the objects for the ClustAssess ShinyApp

Description

Given the output of the ClustAssess pipeline, the expression matrix and the metadata, this function creates the files needed for the ClustAssess ShinyApp. The files are written in the project_folder and are the following:

• metadata.rds: the metadata file

• stability.h5: contains the stability results

• expression.h5: contains the expression matrix and the rank matrix

Usage

write_objects(
  clustassess_object,
  expression_matrix,
  metadata,
  project_folder = ".",
  compression_level = 6,
  chunk_size = 100,
  gene_variance_threshold = 0,
  summary_function = stats::median,
  qualpalr_colorspace = "pretty"
)

Arguments

clustassess_object	The output of the ClustAssess automatic pipeline
expression_matrix	The expression matrix
metadata	The metadata
project_folder	The folder where the files will be written
compression_level	The compression level for the h5 files (See 'rhdf5::h5createFile“ for more details)
chunk_size	The chunk size for the rank matrix (See rhdf5::h5createDataset for more details)
gene_variance_threshold	The threshold for the gene variance; genes with variance below this threshold will be removed
summary_function	The function used for summarizing the stability values; the default is median
qualpalr_colorspace	The colorspace used for generating the colors; the default is pretty

Value

NULL (the files are written in the project_folder)

Core-Bioinformatics/ClustAssess documentation built on Dec. 19, 2024, 8:19 p.m.