R: Metabolic Pathway Completeness and Abundance Calculation

# Metabolic Pathway Completeness and Abundance Calculation

## Documentation for package ‘mclink’ version 1.1.1

- DESCRIPTION file
- Package README

## 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