calc_data_summary: Create a Data Summary Table for Element Ratios and Parameters

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

Create a Data Summary Table for Element Ratios and Parameters

Description

Generates a data summary table that provides intensity-weighted averages for element ratios, mass accuracy, and additional parameters. Results can be grouped based on the specified grouping columns.

Usage

calc_data_summary(mfd, grp = "file_id", ...)

Arguments

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.
grp	Character vector. Names of columns (e.g., sample or file identifiers) used to aggregate results.
...	Additional arguments passed to methods.

Details

This function computes a variety of weighted averages and summary statistics for mass spectrometry data using the provided peak list (mfd). Calculated values include weighted averages for elemental counts (e.g., Carbon, Hydrogen), elemental ratios (e.g., O/C, H/C), and additional parameters such as the base peak intensity and summed intensities. It also calculates the aromaticity index (wa(AI)) based on the elemental composition. If grouping columns are provided, the summary statistics are calculated for each group.

The function also joins additional indices (ideg, iterr) from related functions calc_ideg() and calc_iterr() to the final summary table.

Value

A data.table containing the summarized results, with columns including:

n(mf)

Number of molecular formulas per group.

accuracy (median)

Median accuracy in parts-per-million (ppm) for the identified peaks.

accuracy (3 sigma cut-off)

Maximum ppm accuracy within a three-sigma range.

wa(mz)

Weighted average m/z value.

wa(DBE)

Weighted average Double Bond Equivalent (DBE).

wa(element)

Weighted averages for elements (C, H, N, O, P, S) and ratios (O/C, H/C, N/C, S/C).

wa(NOSC)

Weighted average nominal oxidation state of carbon.

wa(delG0_Cox)

Weighted average Gibbs free energy (Cox) in kJ/mol.

wa(AI)

Weighted average aromaticity index.

wa(C/N) and wa(C/S)

Ratios derived from N/C and S/C.

ideg, ideg_n

Indices for degree of identification, as calculated by calc_ideg().

iterr, iterr_n, iterr2, iterr2_n

Iteration error indices from calc_iterr().

median(i_magnitude)

Median intensity value.

int(basepeak)

Intensity of the base peak.

int(summed)

Summed intensity of all peaks.

See Also

Other calculations: calc_dbe(), calc_eval_params(), calc_exact_mass(), calc_ideg(), calc_ma(), calc_neutral_mass(), calc_nm(), calc_norm_int(), calc_number_assignment(), calc_number_occurrence(), calc_recalibrate_ms()

Examples

# Example using demo data, grouping by file ID
calc_data_summary(mfd = mf_data_demo, grp = c("file_id"))

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