Man pages for USEPA/LUMA
LCMS-Based Untargeted Metabolomics Assistant
| AnnotatePeaklist | Annotates Peak.list with In House Library |
| calc_corrstat | Calculate correlation matrices for metabolite groups |
| calc_cv | Calculate coeffient of variation (CV) by pooled QCs |
| calc_minfrac | Calculate minimum fraction of features across sample classes |
| CAMERAFiles_dlg | CAMERA Files Dialog Box |
| CombineFeatures | Combines Features into Metabolites |
| combine_ion_modes | Combines Peak.lists from Two Ionization Modes |
| CombinePeaklists | Combine Peaklists from different ion modes |
| combine_phenodata | Combine phenotype data in Peak.list |
| connect_libdb | Connects to library database |
| connect_lumadb | Connects to LUMA database |
| connect_peakdb | Connects to peak database |
| CullBackground | Culls the Peak.list by Background |
| CullCV | Culls the Peak.list by Percent CV |
| CullMF | Culls the Peak.list by Minimum Fraction |
| CullVoidVolume | Culls the Peak.list by Void volume |
| FinalWorkflow | Constructor module to finalize LUMA workflow |
| find_Background | Finds background components in Peak.list |
| FormatForMetaboAnalystR | Formatting of metabolite data for MetaboAnalystR. |
| FormatForSIMCA | Format Peaklists for input into SIMCA |
| format_MetabolomicData | Formatting of metabolomic data for MetaboAnalystR. |
| format_simca | Formats Peak.list for SIMCA |
| gen_filebase | Generate Filebase |
| get_features | Retrieves features from Peak.list in a database |
| InitWorkflow | Constructor module to initiate LUMA Workflow |
| InputFiles_dlg | Input Files Dialog Box |
| LUMA-package | LCMS Untargeted Metabolomics Assistant |
| match_Annotation | Matches Peak.list annotations against Annotated Library |
| mSetObj | Example mSetObj |
| NormalizePeaklists | Normalize Peaklists from different ion modes |
| normalize_unit | normalize_unit |
| output_MetaData | Printing metadata as CSV files for MetaboAnalystR. |
| ParseCAMERA | Parses CAMERA annotations |
| parse_neg_results | CAMERA Parser in negative mode |
| parse_pos_results | CAMERA Parser in positive mode |
| Peaklist_Pos | Peaklist_Pos_db Tables |
| plot_ionduplicate | Loop-based EIC Plotter for Ion Mode Duplicates |
| plot_metgroup | Loop-based EIC Plotter for metabolite groups |
| pre_combine_ion_modes | Combines Peak.lists Simply |
| read_tbl | Reads Peak.list from database |
| remove_background_peaks | Removes background components from Peak.list |
| remove_ion_dup | Removes Ion Mode Duplicates |
| remove_void_volume | Removes void volume from Peak.list |
| replace_zeros_normalize | Replaces zeros and normalizes |
| ScriptInfo_dlg | Script Info Dialog Box |
| search_IonDup | Searches Peak.list for ion mode duplicates |
| SimplyPeaklists | Combine Peaklists simply |
| sum_features | Sum features by metabolite group |
| trim_cv | Trims by CV |
| trim_minfrac | Trims by MinFrac |
| trim_rt | Trims by retention time |
| wrap_camera | Wraps CAMERA |
| wrap_xcms | Wraps xcms |
| write_tbl | Writes Peak.list to database |
| write_xlsx | Writes xlsx table |
