mclink (version 1.1.1)

process_module_loop_plu_comma: Process Module Components with Plus and Comma Handling

Description

Processes a vector of KOs, applying different handling methods depending on whether they contain plus signs, commas, or both. Handles complex pathway definitions with both required components (plus-separated) and alternative forms (comma-separated).

Usage

process_module_loop_plu_comma(
  KO_vector,
  module_abundance,
  process_step_plus,
  process_step_comma,
  process_step_direct,
  aggregrate_rowname = "step_1",
  step_count = 1,
  plus_scale_method,
  comma_scale_method
)

Value

List containing: - abundance_table: Processed abundance values - step_count: Updated step counter - abundance_log: log

Arguments

KO_vector

Character vector of KO identifiers to process

module_abundance

Data frame containing KO abundance data

process_step_plus

Function to handle plus-separated KOs (required components)

process_step_comma

Function to handle comma-separated KOs (alternative forms)

process_step_direct

Function to handle individual KOs

aggregrate_rowname

Base name for row aggregation (default: 'step_1')

step_count

Counter for processing steps (default: 1)

plus_scale_method

Scaling method for plus-separated KOs ("mean", "min", or "max")

comma_scale_method

Scaling method for comma-separated KOs ("sum" or "max")