perform_fpa: Perform Feature-based Pathway Analysis (FPA)

In tidymass/metpath: Pathway analysis for metabolomics data

Perform Feature-based Pathway Analysis (FPA)

Description

This function performs feature-based pathway analysis. It contains metabolite annotation based on ms1, network-based metabolite filtering, metabolic module identification.

Usage

perform_fpa(
  feature_table_marker,
  feature_table_all,
  metabolite_database,
  column = c("rp", "hilic"),
  adduct.table = NULL,
  ms1.match.ppm = 25,
  rt.match.tol = 5,
  mz.ppm.thr = 400,
  threads = 3,
  include_hidden_metabolites = FALSE,
  metabolic_network,
  pathway_database
)

Arguments

feature_table_marker	A data frame of marker features.
feature_table_all	A data frame containing all features.
metabolite_database	A metabolite database object containing metabolite spectra.
column	Character vector specifying the chromatography column type. Default is 'c("rp", "hilic")'.
adduct.table	Optional data frame containing adduct information. Default is 'NULL'.
ms1.match.ppm	Numeric; mass tolerance for MS1 matching in parts per million (ppm). Default is '10'.
rt.match.tol	Numeric; retention time tolerance threshold in seconds. Default is '5'.
mz.ppm.thr	Numeric; M/Z tolerance threshold for filtering in ppm. Default is '400'.
threads	Integer; number of threads to use for parallel processing. Default is '3'.
include_hidden_metabolites	Logical; whether to include hidden metabolites. Default is 'FALSE'.
metabolic_network	A metabolic network object representing metabolic reactions.
pathway_database	A pathway database object containing metabolic pathways.

Value

A list containing: - 'metabolic_module_result': A data frame with metabolic module information. - 'final_metabolic_network': A 'tbl_graph' object representing the final metabolic network. - 'annotation_table_final': A data frame with final annotated features.

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