Man pages for sneumann/RMassBank
Workflow to process tandem MS files and build MassBank records
| add.formula | Calculations on molecular formulas |
| addMB | MassBank-record Addition |
| addPeaks | Add additional peaks to spectra |
| addPeaksManually | Addition of manual peaklists |
| addProperty | Add and initialize dataframe column |
| aggregateSpectra | Aggregate analyzed spectra |
| analyzeMsMs | Analyze MSMS spectra |
| annotator.default | Generate peak annotation from peaklist |
| archiveResults | Backup 'msmsWorkflow' results |
| checkIsotopes | Checks for isotopes in a 'msmsWorkspace' |
| checkSpectra | Check if a spectra set is found, complete, empty |
| cleanElnoise | Remove electronic noise |
| combineMultiplicities | Combine workspaces for multiplicity filtering |
| createMolfile | Create MOL file for a chemical structure |
| CTS.externalIdSubset | Select a subset of external IDs from a CTS record. |
| CTS.externalIdTypes | Find all available databases for a CTS record |
| dbe | Calculate Double Bond Equivalents |
| deprofile | De-profile a high-resolution MS scan in profile mode. |
| dot-buildRecord.RmbSpectraSet | Compile MassBank records |
| dot-parseTitleString | Parse record title |
| dot-updateObject.RmbSpectrum2.formulaSource | Add formulaSource column to spectrum. |
| exportMassbank | Export internally stored MassBank data to files |
| fillback | Fill back reanalyzed / refiltered peak info into spectra |
| filterLowaccResults | Filter peaks with low accuracy |
| filterMultiplicity | filterMultiplicity |
| filterPeakSatellites | Filter satellite peaks |
| filterPeaksMultiplicity | Multiplicity filtering: Removes peaks which occur only once... |
| findEIC | Extract EICs |
| findMass | Calculate exact mass |
| findMsMsHR | Extract MS/MS spectra for specified precursor |
| findMsMsHR.direct | Discontinued: find MS/MS spectrum from open raw file |
| findMsMsHRperxcms | Read in mz-files using XCMS |
| findMsMsHR.ticms2 | Extract an MS/MS spectrum from MS2 TIC |
| findMz | Find compound information |
| findMz.formula | Find the exact mass +/- a given margin for a given formula or... |
| findProgress | Determine processed steps |
| flatten | Flatten, or re-read, MassBank header blocks |
| formulastring.to.list | Interconvert molecular formula representations |
| gatherData | Retrieve annotation data |
| gatherDataBabel | Retrieve annotation data |
| gatherDataUnknown | Retrieve annotation data |
| gatherPubChem | Retrieve supplemental annotation data from Pubchem |
| getAnalyticalInfo | Compose data block of MassBank record |
| getCactus | Retrieve information from Cactus |
| getCompTox | Retrieves DTXSID (if it exists) from EPA Comptox Dashboard |
| getCSID | Retrieve the Chemspider ID for a given compound |
| getCtsKey | Convert a single ID to another using CTS. |
| getCtsRecord | Retrieve information from CTS |
| getData | Get data frame with all present peak data |
| getMolecule | Create Rcdk molecule from SMILES |
| getPcId | Search Pubchem CID |
| is.valid.formula | Check validity of formula |
| loadInfolists | Load MassBank compound information lists |
| loadList | Load compound list for RMassBank |
| makeMollist | Write list.tsv file |
| makePeaksCache | Generate peaks cache |
| makeRecalibration | Recalibrate MS/MS spectra |
| mbWorkflow | MassBank record creation workflow |
| mbWorkspace-class | Workspace for 'mbWorkflow' data |
| mergePeaks.df | Merge peaks for spectra merging, FT shoulder elimination etc. |
| msmsRead | Extracts and processes spectra from a specified file list,... |
| msmsRead.RAW | Extracts and processes spectra from a list of xcms-Objects |
| msmsWorkflow | RMassBank mass spectrometry pipeline |
| msmsWorkspace-class | Workspace for 'msmsWorkflow' data |
| newMbWorkspace | Create new workspace for 'mbWorkflow' |
| newMsmsWorkspace | Create new empty workspace or load saved data for... |
| order.formula | Order a chemical formula correctly |
| parseMassBank | MassBank-record Parser |
| parseMbRecord | MassBank-record Parser |
| peaksMatched | Select matching/unmatching peaks from aggregate table |
| peaksUnmatched | Select matching/unmatching peaks from aggregate table |
| plotMbWorkspaces | Plots mbWorkspaces |
| plotRecalibration | Plot the recalibration graph. |
| ppm | Calculate ppm values |
| problematicPeaks | Identify intense peaks (in a list of unmatched peaks) |
| processProblematicPeaks | Generate list of problematic peaks |
| progressBarHook | Standard progress bar hook. |
| reanalyzeFailpeaks | Reanalyze unmatched peaks |
| recalibrate | Predefined recalibration functions. |
| recalibrate.addMS1data | Return MS1 peaks to be used for recalibration |
| RmbDefaultSettings | RMassBank settings |
| RmbSettings | RMassBank settings |
| selectPeaks | Select peaks from aggregate table |
| selectSpectra | Select a subset of spectra matching properties |
| setData | Set 'RmbSpectrum2' data from data.frame |
| smiles2mass | Calculate the mass from a SMILES-String |
| spectraCount | Count MS2 spectra per compound |
| to.limits.rcdk | Convert formula to Rcdk limits |
| toMassbank | Write MassBank record into character array |
| toRMB | Conversion of XCMS-pseudospectra into RMassBank-spectra |
| updateSettings | Update settings to current version |
| validate | Validate MassBank records with a set of Unit tests |
