annotate_metabolites_fpa: Annotate Metabolites for Feature Pathway Analysis (FPA)

In tidymass/metpath: Pathway analysis for metabolomics data

Annotate Metabolites for Feature Pathway Analysis (FPA)

Description

This function performs metabolite annotation for a given feature table using an MS1-based approach. It processes both positive and negative ionization modes separately and extracts annotation results.

Usage

annotate_metabolites_fpa(
  feature_table,
  metabolite_database,
  column = c("rp", "hilic"),
  adduct.table = NULL,
  ms1.match.ppm = 10,
  rt.match.tol = 5,
  mz.ppm.thr = 400,
  threads = 3
)

Arguments

feature_table	A data frame containing feature data, including 'variable_id', 'mz', 'rt', and 'polarity' columns.
metabolite_database	A metabolite database object used for annotation.
column	A character string specifying the chromatography column type. Options are '"rp"' (reverse phase) or '"hilic"' (hydrophilic interaction chromatography). Default is '"rp"'.
adduct.table	Optional data frame specifying possible adducts. 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 for matching in seconds. Default is '5'.
mz.ppm.thr	Numeric; M/Z tolerance threshold for filtering in ppm. Default is '400'.
threads	Integer; number of parallel threads to use for annotation. Default is '3'.

Value

A data frame containing the annotated metabolites with polarity information.

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