add.formula | Calculations on molecular formulas |
addPeaks | Add additional peaks to spectra |
aggregateSpectra | Aggregate analyzed spectra |
analyzeMsMs | Analyze MSMS spectra |
archiveResults | Backup 'msmsWorkflow' results |
cleanElnoise | Remove electronic noise |
compileRecord | Compile MassBank records |
createMolfile | Create MOL file for a chemical structure |
dbe | Calculate Double Bond Equivalents |
deprofile | De-profile a high-resolution MS scan in profile mode. |
deprofile.fwhm | De-profile a high-resolution MS scan in profile mode. |
deprofile.localMax | De-profile a high-resolution MS scan in profile mode. |
deprofile.scan | De-profile a high-resolution MS scan in profile mode. |
deprofile.spline | De-profile a high-resolution MS scan in profile mode. |
exportMassbank | Export internally stored MassBank data to files |
filterLowaccResults | Filter peaks with low accuracy |
filterMultiplicity | filterMultiplicity |
filterPeakSatellites | Filter satellite peaks |
filterPeaksMultiplicity | Multiplicity filtering: Removes peaks which occur only once in a n-spectra set. |
findCAS | Find compound information |
findEIC | Extract EICs |
findFormula | Find compound information |
findMass | Calculate exact mass |
findMsMsHR | Extract MS/MS spectra for specified precursor |
findMsMsHR.direct | Extract MS/MS spectra for specified precursor |
findMsMsHR.mass | Extract MS/MS spectra for specified precursor |
findMz | Find compound information |
findMz.formula | Find the exact mass +/- a given margin for a given formula or its ions and adducts. |
findName | Find compound information |
findRt | Find compound information |
findSmiles | Find compound information |
flatten | Flatten, or re-read, MassBank header blocks |
formulastring.to.list | Interconvert molecular formula representations |
gatherCompound | Compose data block of MassBank record |
gatherData | Retrieve annotation data |
gatherSpectrum | Compose data block of MassBank record |
getCactus | Retrieve information from Cactus |
getCtsRecord | Retrieve information from CTS |
getMolecule | Create Rcdk molecule from SMILES |
getPcId | Search Pubchem CID |
is.valid.formula | Check validity of formula |
list.to.formula | Interconvert molecular formula representations |
loadInfolist | Load MassBank compound information lists |
loadInfolists | Load MassBank compound information lists |
loadList | Load compound list for RMassBank |
loadMsmsWorkspace | Create new empty workspace or load saved data for 'msmsWorkflow' |
loadRmbSettings | RMassBank settings |
loadRmbSettingsFromEnv | RMassBank settings |
makeMollist | Write list.tsv file |
makeRecalibration | Recalibrate MS/MS spectra |
mbWorkflow | MassBank record creation workflow |
mbWorkspace-class | Workspace for 'mbWorkflow' data |
msmsWorkflow | RMassBank mass spectrometry pipeline |
msmsWorkspace-class | Workspace for 'msmsWorkflow' data |
multiply.formula | Calculations on molecular formulas |
newMbWorkspace | Create new workspace for 'mbWorkflow' |
newMsmsWorkspace | Create new empty workspace or load saved data for 'msmsWorkflow' |
order.formula | Order a chemical formula correctly |
ppm | Calculate ppm values |
problematicPeaks | Identify intense peaks (in a list of unmatched peaks) |
readMbdata | Flatten, or re-read, MassBank header blocks |
reanalyzeFailpeak | Reanalyze unmatched peaks |
reanalyzeFailpeaks | Reanalyze unmatched peaks |
recalibrate | Predefined recalibration functions. |
recalibrate.addMS1data | Return MS1 peaks to be used for recalibration |
recalibrate.loess | Predefined recalibration functions. |
recalibrateSingleSpec | Recalibrate MS/MS spectra |
recalibrateSpectra | Recalibrate MS/MS spectra |
resetInfolists | Load MassBank compound information lists |
resetList | Load compound list for RMassBank |
RmbDefaultSettings | RMassBank settings |
RmbSettings | RMassBank settings |
RmbSettingsTemplate | RMassBank settings |
show-method | Workspace for 'mbWorkflow' data |
show-method | Workspace for 'msmsWorkflow' data |
to.limits.rcdk | Convert formula to Rcdk limits |
toMassbank | Write MassBank record into character array |