generate_null_activity_score_distribution: Generate Null Distribution of Activity Scores

generate_null_activity_score_distributionR Documentation

Generate Null Distribution of Activity Scores

Description

This function generates a null distribution of activity scores by performing random sampling of marker metabolites and calculating activity scores through network analysis.

Usage

generate_null_activity_score_distribution(
  annotation_table_all,
  feature_table_marker,
  metabolite_database,
  metabolic_network,
  permutation_times = 20,
  threads = 8,
  adduct.table = NULL,
  column = c("rp", "hilic"),
  ms1.match.ppm = 25,
  mz.ppm.thr = 400,
  include_hidden_metabolites = FALSE
)

Arguments

annotation_table_all

A data frame containing all annotated metabolites.

feature_table_marker

A data frame containing marker features.

metabolite_database

A metabolite database object used for annotation.

metabolic_network

An 'igraph' object representing the metabolic network.

permutation_times

Integer; number of permutations to perform. Default is '20'.

threads

Integer; number of parallel threads to use. Default is '8'.

adduct.table

Optional data frame specifying possible adducts. Default is 'NULL'.

column

Character; chromatography column type. Options are '"rp"' or '"hilic"'. Default is '"rp"'.

ms1.match.ppm

Numeric; MS1 matching tolerance in ppm. Default is '25'.

mz.ppm.thr

Numeric; M/Z tolerance threshold in ppm. Default is '400'.

include_hidden_metabolites

Logical; whether to include hidden metabolites in the network analysis. Default is 'FALSE'.

Value

A list of numeric vectors representing null activity scores for each permutation.


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