ume_assign_formulas: Complete formula assignment (wrapper function)

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Complete formula assignment (wrapper function)

Description

Assigns molecular formulas to neutral molecular masses and calculates all parameters required for data evaluation, such as a posteriori filtering of molecular formulas, plotting, and statistics. The function uses a pre-build molecular formula library.

Usage

ume_assign_formulas(pl, formula_library, verbose = FALSE, ...)

Arguments

pl	data.table containing peak data. Mandatory columns include neutral molecular mass (mass), peak magnitude (i_magnitude), and a peak identifier (peak_id).
formula_library	Molecular formula library: a predefined data.table used for assigning molecular formulas to a peak list and for mass calibration. The library requires a fixed format, including mass values for matching. Predefined libraries are available in the R package ume.formulas and further described in Leefmann et al. (2019). A standard library for marine dissolved organic matter is ume.formulas::lib_02. New libraries can be built using ume::create_ume_formula_library().
verbose	logical; if TRUE, show progress messages.
...	Arguments passed on to calc_ma_abs, calc_neutral_mass, assign_formulas, eval_isotopes, calc_eval_params, add_known_mf, calc_norm_int m Measured mass ma_dev Mass accuracy in +/- parts per million (ppm) mz Numeric vector of m/z values (> 0). pol Character: "neg", "pos", or "neutral". remove_isotopes If set to TRUE (default), all entries for isotopologues are removed from mfd. The main isotope information for each parent ion is still maintained in the "intxy"-columns. mfd data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula. mf_col Name of the column in mfd that has the molecular formula information (default: "mf"). Formulas have upper case element symbols and elements in the formula are ordered according to the Hill system. known_mf data.table with known molecular formulas (ume::known_mf). ms_id Character; name of the column identifying individual spectra (default: "file_id"). peak_id Character; name of the column identifying unique peaks (default: "peak_id"). peak_magnitude Character; name of the column containing peak intensity values (default: "i_magnitude"). normalization Character; normalization method to apply. One of "bp", "sum", "sum_ubiq", "sum_rank", "none". Default is "bp". n_rank Integer; number of top-ranked peaks to use for "sum_rank" normalization (default: 200).

Details

All function arguments: args(filter_mf_data) args(filter_int)

Value

A data.table having molecular formula assignments for each mass.

See Also

Other Formula assignment: add_known_mf(), calc_eval_params(), check_formula_library(), eval_isotopes()

Other Formula subsetting: filter_int(), filter_mass_accuracy(), filter_mf_data(), remove_blanks(), subset_known_mf(), ume_filter_formulas()

Other ume wrapper: ume_filter_formulas()

Examples

ume_assign_formulas(pl = peaklist_demo, formula_library = lib_demo, pol = "neg", ma_dev = 0.2)

ume documentation built on Dec. 13, 2025, 1:06 a.m.