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Get Metabolite Isomers and Isobars

get_metabo_iso.Rd

This function retrieves metabolite isomers and isobars for a given list of sum formula, considering various parameters such as adducts, polarization mode, and mass range.

Usage

get_metabo_iso(
  sf_vec,
  consider_isobars = T,
  polarization_mode = NA,
  mass_range_ppm = 3,
  annot_db = "HMDB",
  annot_custom_db = NULL,
  use_LION = F,
  endogenous_only = T,
  pathway_assoc_only = F,
  remove_expected_predicted = T
)

Arguments

sf_vec

A character vector of metabolite formulas with optional adducts. The formulas should be formatted as formula[+adduct] or formula[-adduct].

consider_isobars

A logical indicating whether to consider isobars. If TRUE, the function will identify and include isobars based on the provided mass range.

polarization_mode

A character string specifying the ionization mode. Options are "positive" or "negative". Only relevant if consider_isobars is TRUE.

mass_range_ppm

A numeric value specifying the mass range in parts per million (ppm) for identifying isobars.

annot_db

A character vector specifying the annotation databases to use. Options include "HMDB", "LipidMaps", "SwissLipids", and "CoreMetabolome".

annot_custom_db

A custom annotation database. If not NULL, this custom database will be used instead of the specified annotation databases.

use_LION

A logical indicating whether to use the LION version of the LipidMaps database if "LipidMaps" is included in annot_db.

endogenous_only

A logical indicating whether to include only endogenous metabolites. Applies only to "HMDB" and "CoreMetabolome".

pathway_assoc_only

A logical indicating whether to include only metabolites associated with pathways. Applies only to "HMDB" and "CoreMetabolome".

remove_expected_predicted

A logical indicating whether to remove metabolites with a status of "expected" or "predicted" in HMDB and CoreMetabolome databases.

Value

A named list where each element corresponds to a formula from sf_vec. Each element is a character vector containing metabolite names matching the formula and its isobars, if consider_isobars is TRUE.

Details

This function processes a vector of metabolite formulas and retrieves the corresponding metabolite names from the specified annotation databases. If consider_isobars is TRUE, it will also find isobars based on the specified mass range and polarization mode.

Examples

if (FALSE) { # \dontrun{
sf_vec <- c("C6H12O6+H", "C6H12O6-H")
results <- get_metabo_iso(
  sf_vec,
  consider_isobars = TRUE,
  polarization_mode = "positive",
  mass_range_ppm = 5
)
} # }