calculate_activity_socre: Calculate Activity Score for Metabolic Modules

In tidymass/metpath: Pathway analysis for metabolomics data

Calculate Activity Score for Metabolic Modules

Description

This function calculates an activity score for each metabolic module based on its detected and hidden metabolites, as well as its structure within a sub-metabolic network. The calculation incorporates modularity and degree-based weighting to assess the significance of the module.

Usage

calculate_activity_socre(
  metabolic_modules,
  detected_metabolites,
  hidden_metabolites,
  sub_metabolic_network,
  threads = 3
)

Arguments

metabolic_modules	A list of metabolic modules, where each module is represented as a vector of metabolite IDs.
detected_metabolites	A character vector of detected metabolite IDs.
hidden_metabolites	A character vector of hidden metabolite IDs.
sub_metabolic_network	An 'igraph' object representing the sub-metabolic network.
threads	An integer specifying the number of threads to use for parallel computation. Default is 3.

Details

The activity score is computed by assessing the modularity of each metabolic module within the sub-metabolic network. The function extracts the subgraph corresponding to each module and computes a modularity-based score adjusted for the total number of metabolites in the dataset.

The computation is performed in parallel using 'BiocParallel', selecting either 'MulticoreParam' (for Unix-based systems) or 'SnowParam' (for Windows) to handle multi-threaded execution efficiently.

Value

A numeric vector where each value represents the activity score of a corresponding metabolic module.

Examples

## Not run: 
library(igraph)

# Example metabolic network
g <- make_ring(10)
V(g)$name <- paste0("M", 1:10)

# Example input data
metabolic_modules <- list(
  c("M1", "M2", "M3"),
  c("M4", "M5", "M6", "M7")
)
detected_metabolites <- c("M1", "M3", "M5", "M7")
hidden_metabolites <- c("M2", "M6")

# Compute activity scores
scores <- calculate_activity_score(
  metabolic_modules = metabolic_modules,
  detected_metabolites = detected_metabolites,
  hidden_metabolites = hidden_metabolites,
  sub_metabolic_network = g,
  threads = 2
)

print(scores)

## End(Not run)

tidymass/metpath documentation built on June 1, 2025, 10:05 p.m.