Learn R Programming

An R package for UltraMassExplorer (UME)

Copy Link

Version

Install

install.packages('ume')

Version

1.5.2

License

MIT + file LICENSE

Homepage

https://gitlab.awi.de/bkoch/ume

Maintainer

Boris Koch

Last Published

December 12th, 2025

Functions in ume (1.5.2)

Calculate absolute mass accuracy range (ma)

Check format of molecular formula data

Classify FTMS files into categories based on filename patterns

Create a Custom Interpolated Color Palette

.palette_builders

CENTRAL PALETTE REGISTRY

convert_molecular_formula_to_data_table

Convert Molecular Formulas to a Data Table of Element Counts

.prepare_peaklist_columns

Ensure required peaklist columns are present

calc_simpson_index

Calculate the Simpson Diversity Index

f_colpal_selection

Retrieve a Palette and a Representative Default Color

convert_data_table_to_molecular_formulas

Convert Data Table with Element Counts to Molecular Formulas

Internal helper: pretty label lookup

.filter_peaklist_basic

Apply basic filters to peaklist

check_formula_library

Check format of formula library

create_ume_formula_library

Create a molecular formula library for UME

download_library

Download and Load a UME Formula Library from Zenodo

.ume_schema_peaklist

Data table schemas used in ume

Create Customized Color Scales

Conditional message output for verbose functions

check_table_schema

Check data.table structure

create_custom_formula_library

Create a custom molecular formula library for UltraMassExplorer

extract_metadata_from_ufz_files

Extract Metadata from UFZ FTMS Filenames

is_ume_peaklist

Check whether an object is a UME peaklist

filter_mass_accuracy

Automated filter for mass accuracy

extract_aquisition_params

Extract Acquisition Parameters from a Bruker PDF Report

extract_aquisition_params_from_folder

Extract Acquisition Parameters from All PDF Files in a Folder

Filter by (relative) peak magnitude

get_isotope_info

Retrieve NIST element and isotope data

.load_peaklist_file

Load a peaklist from file

.as_peaklist_from_numeric

Convert numeric m/z vector into minimal peaklist

Demo formula library (200 - 300 Da, neutral mass)

Remove molecular formulas detected in blanks

Kendrick Mass Defect (KMD) vs. Nominal Mass Plot

Filter molecular formula data by mass spectrometric metadata

Collection of known formulas, for which additional information is available.

Masses: Elements and isotopes

.extract_library_version

Extract UME library version from formula library object

Internal: Apply UME layout styling to plotly figures

uplot_dbe_minus_o_freq

Frequency Plot of DBE - O

Plot DBE vs Carbon Atoms

remove_empty_columns

Remove empty columns

Plot Median of Mass Accuracy per Sample (ppm)

read_xml_peaklist

Read xml peaklists generates ultrahigh-resolution MS analyses

revert_column_names

Revert data.table column names

uplot_freq_vs_ppm

Mass Accuracy Frequency Histogram

export_ume_results

Export UME Analysis Results

Evaluate isotope information

Common parameters for ume package functions

load_ume_results

load_ume_results

H/C vs Molecular Mass Plot

Plot of Molecular Mass (M) vs. Number of Carbon Atoms (C)

Outlier detection using multiple statistical tests

Plot DBE vs Oxygen Atoms (cf. Herzsprung et al. 2014) with Option for Interactive Plot

uplot_dbe_vs_ppm

Plot DBE vs ppm with Option for Interactive Plot

uplot_n_mf_per_sample

Number of Molecular Formulas per Sample Plot

Plot Mass Spectrum

Molecular Formula Ratio Plot (Sample vs Control)

validate_peaklist

Validate UME peaklist structure

subset_known_mf

Subsetting known molecular formula categories

uplot_reproducibility

Check Reproducibility of Sample Analyses

Histogram of Mass Accuracy

Frequency Plot of a Selected Variable

Labels of UME columns.

uplot_ri_vs_sample

Average Relative Intensity per Sample

Plot LC-MS Spectrum (or fallback MS if no RT available)

Plot Mass Accuracy vs m/z

remove_id_columns

Remove columns that contain ID's

uplot_isotope_precision

Precision of Isotope Abundance

uplot_heteroatoms

Heteroatom Combination vs Mass Accuracy

remove_unknown_columns

Remove columns that only have one specific value

ume_filter_formulas

Complete Formula subsetting / filtering (wrapper)

ume_assign_formulas

Complete formula assignment (wrapper function)

calc_eval_params

Calculate UME Evaluation Parameters

Check format of peaklist

Calculate Double Bond Equivalent (DBE)

calc_exact_mass

Calculate Exact Monoisotopic Mass of a Molecule

assign_formulas

Molecular Formula Assignment

Add metainformation derived from ume::known_mf

calc_data_summary

Create a Data Summary Table for Element Ratios and Parameters

Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)

add_missing_element_columns

Add Missing Isotope Columns to mfd

Calculate Normalized Peak Intensities

calc_recalibrate_ms

Recalibrate mass spectra

Calculate Degradation Index (Ideg)

Calculate mass accuracy

calc_neutral_mass

Calculate neutral molecular mass

calc_number_assignment

Calculate Number of Molecular Formula Assignments per Peak

calc_shannon_index

Calculate the Shannon Diversity Index

Calculate Nominal Mass of a Molecule

calc_pielou_evenness

Calculate Pielou's Evenness

calc_number_occurrence

Calculate number of molecular formulas that were assigned to a molecular mass.