Metabolic Pathway Completeness and Abundance Calculation

---

Documentation for package ‘mclink’ version 1.1

• DESCRIPTION file.

Help Pages

add_rows_if_not_exists	Add Missing Rows to a Data Frame
ata_cal	Calculate Log2 Ratio of Sample Values to Row Means
convert_abundance_to_presence	Convert Abundance Values to Presence/Absence Indicators
create_sub_module_sample	Create and Export Pathway-Specific Module Sample Files
escape_special_chars	Escape Special Characters in a String
extract_inner_brackets	Extract Innermost Parentheses Content
group_ko_by_module	Group KO Abundance Data by Module
KO_pathway_ref	KEGG Orthology (KO) Pathway Information Dataset
KO_Sample_wide	KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes
mclink	Metabolic Pathway Coverage Analysis
merge_module_name	Merge Module Information with Module Table
process_all_modules	Process All Modules in Pathway Information
process_all_pathways	Process All Pathways Analysis
process_module_brackets	Process Module Brackets Recursively
process_module_definition	Process Module Definition String
process_module_loop_comma	Process Module Components with Comma Handling
process_module_loop_plus	Process Module Components with Plus Sign Handling
process_module_loop_plu_comma	Process Module Components with Plus and Comma Handling
process_module_step	Process Module Steps with Complex KO String Handling
process_module_structure	Process Module Structure Data
process_step_comma	Process Comma-Separated KOs with Specified Scaling Method
process_step_direct	Direct KO Processing Without Special Handling
process_step_plus	Process Plus-Separated KOs with Specified Scaling Method
process_step_space	Process Space-Separated KOs with Mean Calculation
read_and_process_KO_table	Read and Process KO Sample Table with Pathway Information
read_and_process_pathway_infor	Read and process Pathway information dataframe
remove_outer_brackets	Remove Outer Parentheses from String