# R Access to Mass-Spec Data

## Documentation for package ‘RaMS’ version 1.4.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

$.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 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
[.msdata_connection | S3 indexing for msdata_connection objects