Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

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Documentation for package ‘ume’ version 1.5.2

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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_peaklist Check format of peaklist
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_iterr Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)
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
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_ume_formula_library Create a molecular formula library for UME
download_library Download and Load a UME Formula Library from Zenodo
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
get_isotope_info Retrieve NIST element and isotope data
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
nice_labels_dt nice_labels_dt
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
tab_ume_labels Labels of UME columns.
theme_uplots theme_uplots
ume_assign_formulas Complete formula assignment (wrapper function)
ume_filter_formulas Complete Formula subsetting / filtering (wrapper)
uplot_cluster uplot_cluster
uplot_cvm Plot of Molecular Mass (M) vs. Number of Carbon Atoms (C)
uplot_dbe_minus_o_freq Frequency Plot of DBE - O
uplot_dbe_vs_c Plot DBE vs Carbon Atoms
uplot_dbe_vs_o 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_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 uplot_pca
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 Average Relative Intensity per Sample
uplot_vk uplot_vk
ustats_outlier Outlier detection using multiple statistical tests