generate_null_activity_score_distribution: Generate Null Distribution of Activity Scores

In tidymass/metpath: Pathway analysis for metabolomics data

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.