write_objects {ClustAssess} | R Documentation |
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 |
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 |
qualpalr_colorspace |
The colorspace used for generating the colors; the default is |
Value
NULL (the files are written in the project_folder)