| Add a negative mass shift to a list of spectra | -,RmbSpectraSet,ANY-method |
| Add a negative mass shift to a list of spectra | -,RmbSpectrum2List,ANY-method |
| Add a negative mass shift to a spectrum | -,Spectrum,numeric-method |
| Parse record title | .parseTitleString |
| Add formulaSource column to spectrum. | .updateObject.RmbSpectrum2.formulaSource |
| Add a mass shift to a list of spectra | +,RmbSpectraSet,ANY-method |
| Add a mass shift to a list of spectra | +,RmbSpectrum2List,ANY-method |
| Add a mass shift to a spectrum | +,Spectrum,numeric-method |
| Calculations on molecular formulas | add.formula multiply.formula |
| MassBank-record Addition | addMB |
| Add additional peaks to spectra | addPeaks |
| Addition of manual peaklists | addPeaksManually |
| Add and initialize dataframe column | addProperty addProperty,data.frame,character,character-method addProperty,RmbSpectrum2,character,character-method |
| Aggregate analyzed spectra | aggregateSpectra |
| Analyze MSMS spectra | analyzeMsMs analyzeMsMs.formula analyzeMsMs.intensity |
| Generate peak annotation from peaklist | annotator.default |
| Backup 'msmsWorkflow' results | archiveResults |
| Build MassBank records | buildRecord buildRecord,RmbSpectraSet-method buildRecord,RmbSpectrum2-method |
| Convert CAS to SMILES | CAS2SMILES |
| Checks for isotopes in a 'msmsWorkspace' | checkIsotopes |
| Check if a spectra set is found, complete, empty | checkSpectra checkSpectra,RmbSpectraSet,character-method |
| Remove electronic noise | cleanElnoise cleanElnoise,data.frame,numeric,numeric-method cleanElnoise,RmbSpectraSet,numeric,numeric-method cleanElnoise,RmbSpectrum2,numeric,numeric-method cleanElnoise,RmbSpectrum2List,numeric,numeric-method |
| Combine workspaces for multiplicity filtering | combineMultiplicities |
| Convert a Compoundlist into an SDF | compoundlist2SDF |
| Create a Compoundlist from JCAMP files | createCompoundlist |
| Create MOL file for a chemical structure | createMolfile |
| Select a subset of external IDs from a CTS record. | CTS.externalIdSubset |
| Find all available databases for a CTS record | CTS.externalIdTypes |
| Calculate Double Bond Equivalents | dbe |
| De-profile a high-resolution MS scan in profile mode. | deprofile deprofile.fwhm deprofile.localMax deprofile.scan deprofile.spline |
| Export internally stored MassBank data to files | exportMassbank |
| Fill back reanalyzed / refiltered peak info into spectra | fillback fillback,msmsWorkspace,missing,missing-method fillback,RmbSpectraSet,missing,data.frame-method fillback,RmbSpectrum2,character,data.frame-method |
| Filter a Compoundlist for missing SMILES values | filterCompoundlist |
| Filter peaks with low accuracy | filterLowaccResults |
| filterMultiplicity | filterMultiplicity |
| Filter satellite peaks | filterPeakSatellites |
| Multiplicity filtering: Removes peaks which occur only once in a n-spectra set. | filterPeaksMultiplicity |
| Extract EICs | findEIC |
| Calculate exact mass | findMass |
| Extract MS/MS spectra for specified precursor | findMsMsHR findMsMsHR.mass |
| Discontinued: find MS/MS spectrum from open raw file | findMsMsHR.direct |
| Extract an MS/MS spectrum from MS2 TIC | findMsMsHR.ticMS2 findMsMsHR.ticms2 |
| Retrieve spectra from msp files | findMsMsHRperMsp findMsMsHRperMsp.direct |
| Read in mz-files using XCMS | findMsMsHRperxcms findMsMsHRperxcms.direct |
| Find compound information | findCAS findFormula findLevel findMz findName findRt findSmiles |
| Find the exact mass +/- a given margin for a given formula or its ions and adducts. | findMz.formula |
| Determine processed steps | findProgress |
| Flatten, or re-read, MassBank header blocks | flatten readMbdata |
| Interconvert molecular formula representations | formulastring.to.list list.to.formula |
| Retrieve supplemental annotation data from US EPA | gatherCCTE |
| Retrieve annotation data | gatherData |
| Retrieve annotation data | gatherDataBabel |
| Retrieve annotation data | gatherDataUnknown |
| Retrieve supplemental annotation data from Pubchem | gatherPubChem |
| Get analytical info for MassBank record | getAnalyticalInfo |
| Retrieve information from Cactus | getCactus |
| Search CCTE CAS registration number | getCASRN |
| Retrieve the Chemspider ID for a given compound | getCSID |
| Convert a single ID to another using CTS. | getCtsKey |
| Retrieve information from CTS | getCtsRecord |
| Get data frame with all present peak data | getData getData,RmbSpectrum2-method |
| Search CCTE DTXCID | getDTXCID |
| Search CCTE DTXSID | getDTXSID |
| Search CCTE SMILES | getDTXSMILES |
| Get the content of a field in a JCAMP file | getField |
| Create Rcdk molecule from SMILES | getMolecule |
| Search Pubchem CID | getPcId |
| Search CCTE Preferred Name | getPrefName |
| Check validity of formula | is.valid.formula |
| Load MassBank compound information lists | loadInfolist loadInfolists resetInfolists |
| Load compound list for RMassBank | loadList resetList |
| Write list.tsv file | makeMollist |
| Generate peaks cache | makePeaksCache |
| Recalibrate MS/MS spectra | makeRecalibration recalibrateSingleSpec recalibrateSpectra |
| MassBank record creation workflow | mbWorkflow |
| Workspace for 'mbWorkflow' data | mbWorkspace-class show,mbWorkspace-method |
| Merge peaks for spectra merging, FT shoulder elimination etc. | mergePeaks mergePeaks,data.frame-method mergePeaks,matrix-method mergePeaks,RmbSpectrum2-method mergePeaks,Spectrum-method |
| Merge multiple spectra into one | mergeSpectra mergeSpectra,RmbSpectrum2List-method |
| Extracts and processes spectra from a specified file list, according to loaded options and given parameters. | msmsRead |
| Extracts and processes spectra from a list of xcms-Objects | msmsRead.RAW |
| RMassBank mass spectrometry pipeline | msmsWorkflow |
| Workspace for 'msmsWorkflow' data | .msmsWorkspace msmsWorkspace-class show,msmsWorkspace-method |
| Create new workspace for 'mbWorkflow' | newMbWorkspace |
| Create new empty workspace or load saved data for 'msmsWorkflow' | loadMsmsWorkspace newMsmsWorkspace |
| Scale spectrum to specified intensity range | normalize,RmbSpectrum2-method |
| Normalize spectra | normalize,RmbSpectrum2List-method |
| Order a chemical formula correctly | order.formula |
| MassBank-record Parser | parseMassBank |
| MassBank-record Parser | parseMbRecord |
| Select matching/unmatching peaks from aggregate table | peaksMatched peaksMatched,data.frame-method peaksMatched,msmsWorkspace-method |
| Select matching/unmatching peaks from aggregate table | peaksUnmatched peaksUnmatched,data.frame-method peaksUnmatched,msmsWorkspace-method |
| Plots mbWorkspaces | plotMbWorkspaces |
| Plot the recalibration graph. | plotRecalibration plotRecalibration.direct |
| Calculate ppm values | ppm |
| Identify intense peaks (in a list of unmatched peaks) | problematicPeaks |
| Generate list of problematic peaks | processProblematicPeaks |
| Standard progress bar hook. | progressBarHook |
| Get a property of an RmbSpectrum2 object | property property,RmbSpectrum2,character-method |
| Replacement function to set properties of an RmbSpectrum2 object | property<- property<-,RmbSpectrum2,character,logical,character-method property<-,RmbSpectrum2,character,logical,missing-method property<-,RmbSpectrum2,character,missing,character-method property<-,RmbSpectrum2,character,missing,missing-method |
| Reanalyze unmatched peaks | reanalyzeFailpeak reanalyzeFailpeaks |
| Predefined recalibration functions. | recalibrate recalibrate.identity recalibrate.linear recalibrate.loess recalibrate.mean |
| Return MS1 peaks to be used for recalibration | recalibrate.addMS1data |
| Pass arguments to logger::log_debug using custom RMassBank-logging settings | rmb_log_debug |
| Pass arguments to logger::log_error using custom RMassBank-logging settings | rmb_log_error |
| Pass arguments to logger::log_fatal using custom RMassBank-logging settings | rmb_log_fatal |
| Pass arguments to logger::log_info using custom RMassBank-logging settings | rmb_log_info |
| Pass arguments to logger::log_success using custom RMassBank-logging settings | rmb_log_success |
| Pass arguments to logger::log_trace using custom RMassBank-logging settings | rmb_log_trace |
| Pass arguments to logger::log_warn using custom RMassBank-logging settings | rmb_log_warn |
| RMassBank settings | loadRmbSettings loadRmbSettingsFromEnv RmbDefaultSettings RmbSettingsTemplate |
| RMassBank settings | RmbSettings |
| Set of spectra pertaining to one compound | .RmbSpectraSet RmbSpectraSet-class |
| RMassBank Representation of an MSMS Spectrum | .RmbSpectrum2 RmbSpectrum2-class |
| SimpleList specializations | .RmbSpectraSetList .RmbSpectrum2List RmbSpectraSetList RmbSpectraSetList-class RmbSpectrum2List-class |
| Select peaks from aggregate table | selectPeaks selectPeaks,data.frame-method selectPeaks,msmsWorkspace-method selectPeaks,RmbSpectraSet-method selectPeaks,RmbSpectraSetList-method selectPeaks,RmbSpectrum2-method selectPeaks,RmbSpectrum2List-method selectPeaks,Spectrum-method |
| Select a subset of spectra matching properties | selectSpectra selectSpectra,msmsWorkspace,character-method selectSpectra,RmbSpectraSetList,character-method |
| Define a programmatic or gluey ACCESSION builder | setAccessionBuilder |
| Set 'RmbSpectrum2' data from data.frame | setData setData,RmbSpectrum2,data.frame-method |
| Calculate the mass from a SMILES-String | smiles2mass |
| Count MS2 spectra per compound | spectraCount spectraCount,msmsWorkspace-method spectraCount,RmbSpectraSet-method spectraCount,RmbSpectraSetList-method |
| Convert formula to Rcdk limits | to.limits.rcdk |
| Write MassBank record into character array | toMassbank toMassbank,RmbSpectraSet-method toMassbank,RmbSpectrum2-method |
| Conversion of XCMS-pseudospectra into RMassBank-spectra | toRMB |
| Add a header to a Multiblock JCAMP file | updateHeader |
| Update settings to current version | updateSettings |
| Validate MassBank records with a set of Unit tests | validate |
