$.msdata_connection |
S3 dollar sign notation 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 |
grabMzmlMetadata |
Helper function to extract mzML file metadata |
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 |
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 |
grabMzxmlMetadata |
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 |
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 collison 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 collison 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 |
[.msdata_connection |
S3 indexing for msdata_connection objects |