ume (version 1.5.2)

ume_assign_formulas: 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, ...)

Value

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

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)

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)