$.msdata_connection     S3 dollar sign notation for msdata_connection
                        objects
[.msdata_connection     S3 indexing for msdata_connection objects
checkOutputQuality      Check that the output data is properly
                        formatted.
editMSfileRTs           Edit mzML/mzXML file retention times
getEncoded              Convert from compressed binary to R numeric
                        vector
giveEncoding            Convert from R numeric vector to compressed
                        binary
grabAccessionData       Get arbitrary metadata from an mzML file by
                        accession number
grabMSdata              Grab mass-spectrometry data from file(s)
grabMzmlBPC             Grab the BPC or TIC from a file
grabMzmlDAD             Extract the DAD data from an mzML nodeset
grabMzmlData            Get mass-spectrometry data from an mzML file
grabMzmlEncodingData    Helper function to extract mzML file encoding
                        data
grabMzmlMS1             Extract the MS1 data from an mzML nodeset
grabMzmlMS2             Extract the MS2 data from an mzML nodeset
grabMzmlMS3             Extract the MS3 data from an mzML nodeset
grabMzmlMetadata        Helper function to extract mzML file metadata
grabMzxmlBPC            Grab the BPC or TIC from a file
grabMzxmlData           Get mass-spectrometry data from an mzXML file
grabMzxmlEncodingData   Helper function to extract mzXML file metadata
grabMzxmlMS1            Extract the MS1 data from an mzXML nodeset
grabMzxmlMS2            Extract the MS2 data from an mzXML nodeset
grabMzxmlMS3            Extract the MS3 data from an mzXML nodeset
grabMzxmlMetadata       Helper function to extract mzXML file metadata
grabMzxmlSpectraMzInt   Extract the mass-to-charge data from the
                        spectra of an mzXML nodeset
grabMzxmlSpectraPremz   Extract the precursor mass from the spectra of
                        an mzXML nodeset
grabMzxmlSpectraRt      Extract the retention time from the spectra of
                        an mzXML nodeset
grabMzxmlSpectraVoltage
                        Extract the collision energies from the spectra
                        of an mzXML nodeset
grabSpectraInt          Extract the intensity information from the
                        spectra of an mzML nodeset
grabSpectraMz           Extract the mass-to-charge data from the
                        spectra of an mzML nodeset
grabSpectraPremz        Extract the precursor mass from the spectra of
                        an mzML nodeset
grabSpectraRt           Extract the retention time from the spectra of
                        an mzML nodeset
grabSpectraVoltage      Extract the collision energies from the spectra
                        of an mzML nodeset
minifyMSdata            Shrink MS data by including only data points
                        near masses of interest
minifyMzml              Shrink mzML files by including only data points
                        near masses of interest
minifyMzxml             Shrink mzXML files by including only data
                        points near masses of interest
msdata_connection       S3 constructor for msdata_connection
mz_group                Group m/z values into bins of a specified ppm
                        width
node2dt                 Convert node to data.table
pmppm                   Plus/minus parts per million
print.msdata_connection
                        S3 print option for msdata_connection objects
qplotMS1data            Quick plot for MS data
tmzmlMaker              Maker of tmzML documents
trapz                   Trapezoidal integration of mass-spec retention
                        time / intensity values
