R/52_check_parameters_functions.R
check_parameters4annotate_metabolites.RdThis 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.
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
)A `mass_dataset` object containing the MS1, RT, and/or MS2 data for annotation.
A `databaseClass` object containing the reference database for metabolite annotation.
Character vector. Specifies the criteria to base the annotation on. Can include `"ms1"`, `"rt"`, and/or `"ms2"`. Default is `c("ms1", "rt", "ms2")`.
Character. The ionization mode, either `"positive"` or `"negative"`. Default is `"positive"`.
Character. The chromatographic column type, either `"hilic"` or `"rp"` (reversed-phase). Default is `"hilic"`.
A data frame containing the adduct table to be used in the annotation process.
Character or vector. Collision energy values to be used in MS2 matching. Default is `"all"`.
Numeric. The mass tolerance in parts per million (ppm) for MS1 peak matching. Default is 25.
Numeric. The mass tolerance in ppm for MS2 peak matching. Default is 30.
Numeric. m/z threshold for ppm calculation. Default is 400.
Numeric. The score tolerance for MS2 matches. Default is 0.5.
Numeric. Weight for the fraction of matched fragments in the total MS2 score calculation. Default is 0.3.
Numeric. Weight for the forward dot product score in MS2 matching. Default is 0.6.
Numeric. Weight for the reverse dot product score in MS2 matching. Default is 0.1.
Numeric. Retention time matching tolerance in seconds. Default is 30.
Numeric. Weight for MS1 matching in the total score. Must be between 0 and 1. Default is 0.25.
Numeric. Weight for RT matching in the total score. Must be between 0 and 1. Default is 0.25.
Numeric. Weight for MS2 matching in the total score. Must be between 0 and 1. Default is 0.5.
Numeric. The threshold for the total score. Must be between 0 and 1. Default is 0.5.
Numeric. The number of top candidate annotations to retain. Must be greater than 0. Default is 3.
Numeric. The intensity cutoff for removing low-intensity MS2 fragments. Default is 0.
Numeric. The number of threads to use for parallel processing. Must be greater than 0. Default is 3.
The function does not return a value but throws an error if any validation checks fail.
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.
if (FALSE) { # \dontrun{
# 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
)
} # }