Learn R Programming
mclink (version 1.1.1)

process_module_step: Process Module Steps with Complex KO String Handling

Description

Processes a KO string containing various combinations of KOs separated by different operators (commas, plus signs, or spaces). Handles complex pathway definitions with multiple types of relationships between KOs.

Usage

process_module_step(
  module_abundance,
  KO_string = "K03388,K03389+K03390+K14083,K14126+K14127,K14128",
  aggregrate_rowname = "bracket_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

module_abundance

Data frame containing KO abundance data

KO_string

String representation of KO relationships (default: "K03388,K03389+K03390+K14083,K14126+K14127,K14128")

aggregrate_rowname

Base name for row aggregation (default: 'bracket_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")