R Access to Mass-Spec Data

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Documentation for package ‘RaMS’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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 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