Processes module sample data across all pathways with specified scaling methods. Handles different comparison methods and outputs results by pathway.
process_all_pathways(
pathway_infor,
Module_Sample,
out_DIR_Module_Sample_by_pathway,
compare_method = c("log", "avg", "round"),
plus_scale_method,
comma_scale_method
)Main outputs are written to: - Combined module file (All_modules.*.tsv) - Pathway-specific files (via create_sub_module_sample)
Data frame containing pathway information, see examples.
Data frame of module sample data to process
Output directory for pathway-specific results
Comparison method to use: "log" (log10 transform), "avg" (average calculation), or "round" (simple rounding)
Scaling method for plus-separated KOs ("mean", "min", or "max")
Scaling method for comma-separated KOs ("sum" or "max")