Man pages for ume
Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter
| add_known_mf | Add metainformation derived from ume::known_mf |
| add_missing_element_columns | Add Missing Isotope Columns to mfd |
| as_peaklist | Check format of peaklist |
| assign_formulas | Molecular Formula Assignment |
| 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... |
| 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_number_occurrence | Calculate number of molecular formulas that were assigned to... |
| calc_pielou_evenness | Calculate Pielou's Evenness |
| calc_recalibrate_ms | Recalibrate mass spectra |
| calc_shannon_index | Calculate the Shannon Diversity Index |
| calc_simpson_index | Calculate the Simpson Diversity Index |
| check_formula_library | Check format of formula library |
| check_mfd | Check format of molecular formula data |
| check_table_schema | Check data.table structure |
| classify_files | Classify FTMS files into categories based on filename... |
| 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_custom_formula_library | Create a custom molecular formula library for... |
| create_ume_formula_library | Create a molecular formula library for UME |
| dot-as_peaklist_from_numeric | Convert numeric m/z vector into minimal peaklist |
| dot-extract_library_version | Extract UME library version from formula library object |
| dot-filter_peaklist_basic | Apply basic filters to peaklist |
| dot-f_label | Internal helper: pretty label lookup |
| dot-load_peaklist_file | Load a peaklist from file |
| dot-msg | Conditional message output for verbose functions |
| dot-palette_builders | CENTRAL PALETTE REGISTRY |
| dot-prepare_peaklist_columns | Ensure required peaklist columns are present |
| dot-ume_schema_peaklist | Data table schemas used in ume |
| download_library | Download and Load a UME Formula Library from Zenodo |
| eval_isotopes | Evaluate isotope information |
| export_ume_results | Export UME Analysis Results |
| 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 |
| extract_metadata_from_ufz_files | Extract Metadata from UFZ FTMS Filenames |
| f_colorz | Create Customized Color Scales |
| f_colpal_selection | Retrieve a Palette and a Representative Default Color |
| 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... |
| lib_demo | Demo formula library (200 - 300 Da, neutral mass) |
| load_ume_results | load_ume_results |
| main_docu | Common parameters for ume package functions |
| 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 |
| read_xml_peaklist | Read xml peaklists generates ultrahigh-resolution MS analyses |
| 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 |
| revert_column_names | Revert data.table column names |
| 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... |
| 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_layout | Internal: Apply UME layout styling to plotly figures |
| 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 |
| validate_peaklist | Validate UME peaklist structure |
