# Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

## Documentation for package ‘ume’ version 1.7.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

add_known_mf | Add metainformation derived from ume::known_mf
add_missing_element_columns | Add Missing Isotope Columns to mfd
assign_formulas | Molecular Formula Assignment
as_mfd | Coerce input to UME molecular formula data
as_peaklist | Check format of peaklist
as_ume_matrix | Convert molecular formula data to a feature matrix
calc_data_summary | Create a Data Summary Table for Element Ratios and Parameters
calc_dbe | Calculate Double Bond Equivalent (DBE)
calc_eval_params | Calculate UME Evaluation Parameters
calc_exact_mass | Calculate Exact Monoisotopic Mass of a Molecule
calc_ideg | Calculate Degradation Index (Ideg)
calc_isotope_pattern | Calculate Isotope Pattern
calc_iterr | Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)
calc_logratio | calc_logratio
calc_ma | Calculate mass accuracy
calc_ma_abs | Calculate absolute mass accuracy range (ma)
calc_neutral_mass | Calculate neutral molecular mass
calc_nm | Calculate Nominal Mass of a Molecule
calc_norm_int | Calculate Normalized Peak Intensities
calc_number_assignment | Calculate Number of Molecular Formula Assignments per Peak
calc_pielou_evenness | Calculate Pielou's Evenness
calc_shannon_index | Calculate the Shannon Diversity Index
calc_simpson_index | Calculate the Simpson Diversity Index
calc_time_flattened_mfd | Create a time-flattened molecular formula data table
check_neutral_mf | Check neutral molecular formulas
classify_files | Classify FTMS files into categories based on filename patterns
color.palette | Create a Custom Interpolated Color Palette
convert_data_table_to_molecular_formulas | Convert Data Table with Element Counts to Molecular Formulas
convert_molecular_formula_to_data_table | Convert Molecular Formulas to a Data Table of Element Counts
create_isotope_expanded_table | Create an Expanded Table of Parent and Isotope Daughter Formulas
create_time_flattened_mfd | Create a time-flattened molecular formula data table
create_ume_formula_library | Create a molecular formula library for UME
download_library | Download and Load a UME Formula Library
eval_isotopes | Evaluate isotope information
filter_int | Filter by (relative) peak magnitude
filter_mass_accuracy | Automated filter for mass accuracy
filter_mf_data | Filter molecular formula data by mass spectrometric metadata
filter_multi_assignments | Filter multiple molecular formula assignments by mass-error medians
get_isotope_info | Retrieve NIST element and isotope data
inchi_to_mf | Extract molecular formula from InChI string
is_ume_peaklist | Check whether an object is a UME peaklist
known_mf | Collection of known formulas, for which additional information is available.
lib_demo | Demo formula library (200 - 300 Da, neutral mass)
masses | Masses: Elements and isotopes
mf_data_demo | mf_data_demo
order_columns | Order columns
peaklist_demo | Demo peak list
remove_blanks | Remove molecular formulas detected in blanks
remove_empty_columns | Remove empty columns
remove_id_columns | Remove columns that contain ID's
remove_unknown_columns | Remove columns that only have one specific value
subset_known_mf | Subsetting known molecular formula categories
theme_uplots | theme_uplots
ume_assign_formulas | Complete formula assignment (wrapper function)
ume_filter_formulas | Complete Formula subsetting / filtering (wrapper)
ume_name_dictionary | UME name dictionary
uplot_cluster | uplot_cluster
uplot_cvm | Carbon vs Mass (CvM) Diagram
uplot_dbe_minus_o_freq | Frequency Plot of DBE - O atoms
uplot_dbe_vs_c | Plot DBE vs Carbon Atoms
uplot_dbe_vs_ma | Plot DBE vs ppm with Option for Interactive Plot
uplot_dbe_vs_o | Plot DBE vs Oxygen Atoms (cf. Herzsprung et al. 2014) with Option for Interactive Plot
uplot_freq | Frequency Plot of a Selected Variable
uplot_freq_ma | Histogram of Mass Accuracy
uplot_freq_vs_ppm | Mass Accuracy Frequency Histogram
uplot_hc_vs_m | H/C vs Molecular Mass Plot
uplot_heteroatoms | Heteroatom Combination vs Mass Accuracy
uplot_isotope_precision | Precision of Isotope Abundance
uplot_kmd | Kendrick Mass Defect (KMD) vs. Nominal Mass Plot
uplot_lcms | Plot LC-MS Spectrum (or fallback MS if no RT available)
uplot_ma_vs_mz | Plot Mass Accuracy vs m/z
uplot_ms | Plot Mass Spectrum
uplot_n_mf_per_sample | Number of Molecular Formulas per Sample Plot
uplot_pca | Plot PCA Results
uplot_ppm_avg | Plot Median of Mass Accuracy per Sample (ppm)
uplot_ratios | Molecular Formula Ratio Plot (Sample vs Control)
uplot_reproducibility | Check Reproducibility of Sample Analyses
uplot_ri_vs_sample | Median Relative Intensity per Sample
uplot_vk | uplot_vk
ustats_outlier | Outlier detection using multiple statistical tests
zero_filling | zero_filling