check_parameters4annotate_metabolites: Validate Parameters for Metabolite Annotation

In tidymass/metid: Metabolite identification based on MS1 and MS2 spectra

Validate Parameters for Metabolite Annotation

Description

This function validates the input parameters required for the metabolite annotation process. It checks the 'mass_dataset' object, the annotation database, the adduct table, and various matching and weighting parameters to ensure they are correctly specified.

Usage

check_parameters4annotate_metabolites(
  object,
  database,
  based_on = c("ms1", "rt", "ms2"),
  polarity = c("positive", "negative"),
  column = c("hilic", "rp"),
  adduct.table = adduct.table,
  ce = "all",
  ms1.match.ppm = 25,
  ms2.match.ppm = 30,
  mz.ppm.thr = 400,
  ms2.match.tol = 0.5,
  fraction.weight = 0.3,
  dp.forward.weight = 0.6,
  dp.reverse.weight = 0.1,
  rt.match.tol = 30,
  ms1.match.weight = 0.25,
  rt.match.weight = 0.25,
  ms2.match.weight = 0.5,
  total.score.tol = 0.5,
  candidate.num = 3,
  remove_fragment_intensity_cutoff = 0,
  threads = 3
)

Arguments

object	A 'mass_dataset' object containing the MS1, RT, and/or MS2 data for annotation.
database	A 'databaseClass' object containing the reference database for metabolite annotation.
based_on	Character vector. Specifies the criteria to base the annotation on. Can include '"ms1"', '"rt"', and/or '"ms2"'. Default is 'c("ms1", "rt", "ms2")'.
polarity	Character. The ionization mode, either '"positive"' or '"negative"'. Default is '"positive"'.
column	Character. The chromatographic column type, either '"hilic"' or '"rp"' (reversed-phase). Default is '"hilic"'.
adduct.table	A data frame containing the adduct table to be used in the annotation process.
ce	Character or vector. Collision energy values to be used in MS2 matching. Default is '"all"'.
ms1.match.ppm	Numeric. The mass tolerance in parts per million (ppm) for MS1 peak matching. Default is 25.
ms2.match.ppm	Numeric. The mass tolerance in ppm for MS2 peak matching. Default is 30.
mz.ppm.thr	Numeric. m/z threshold for ppm calculation. Default is 400.
ms2.match.tol	Numeric. The score tolerance for MS2 matches. Default is 0.5.
fraction.weight	Numeric. Weight for the fraction of matched fragments in the total MS2 score calculation. Default is 0.3.
dp.forward.weight	Numeric. Weight for the forward dot product score in MS2 matching. Default is 0.6.
dp.reverse.weight	Numeric. Weight for the reverse dot product score in MS2 matching. Default is 0.1.
rt.match.tol	Numeric. Retention time matching tolerance in seconds. Default is 30.
ms1.match.weight	Numeric. Weight for MS1 matching in the total score. Must be between 0 and 1. Default is 0.25.
rt.match.weight	Numeric. Weight for RT matching in the total score. Must be between 0 and 1. Default is 0.25.
ms2.match.weight	Numeric. Weight for MS2 matching in the total score. Must be between 0 and 1. Default is 0.5.
total.score.tol	Numeric. The threshold for the total score. Must be between 0 and 1. Default is 0.5.
candidate.num	Numeric. The number of top candidate annotations to retain. Must be greater than 0. Default is 3.
remove_fragment_intensity_cutoff	Numeric. The intensity cutoff for removing low-intensity MS2 fragments. Default is 0.
threads	Numeric. The number of threads to use for parallel processing. Must be greater than 0. Default is 3.

Details

The function checks the following: * Ensures the 'object' is a valid 'mass_dataset' object and that the 'database' is a valid 'databaseClass' object. * Verifies the presence of required MS1, RT, and MS2 data based on the 'based_on' argument. * Validates the adduct table and checks if collision energy (CE) values match with those in the database. * Ensures that the matching parameters ('ms1.match.ppm', 'ms2.match.ppm', 'mz.ppm.thr', 'ms2.match.tol') are numeric and within valid ranges. * Validates the weights ('ms1.match.weight', 'rt.match.weight', 'ms2.match.weight') and ensures they sum to 1. * Ensures that the number of candidates to retain ('candidate.num') and the number of threads are greater than 0.

Value

The function does not return a value but throws an error if any validation checks fail.

Examples

## Not run: 
# Example usage
check_parameters4annotate_metabolites(
  object = my_dataset,
  database = my_database,
  based_on = c("ms1", "ms2"),
  polarity = "positive",
  column = "rp",
  ms1.match.ppm = 20,
  ms2.match.ppm = 25,
  ms1.match.weight = 0.3,
  rt.match.weight = 0.3,
  ms2.match.weight = 0.4,
  candidate.num = 5,
  threads = 4
)

## End(Not run)

tidymass/metid documentation built on Oct. 8, 2024, 10:32 p.m.