# parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)

## Documentation for package ‘mzR’ version 2.16.0

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

## Help Pages

mzR-package | parser for mzXML, mzData, mzML and mzid files (mass spectrometry data)
analyzer | Access the metadata from an 'mzR' object.
analyzer-method | Class 'mzR' and sub-classes
chromatogram | Access the raw data from an 'mzR' object.
chromatogram-method | Access the raw data from an 'mzR' object.
chromatogramHeader | Access the raw data from an 'mzR' object.
chromatogramHeader-method | Access the raw data from an 'mzR' object.
chromatograms | Access the raw data from an 'mzR' object.
chromatograms-method | Access the raw data from an 'mzR' object.
chromatogramsInfo | Access the metadata from an 'mzR' object.
chromatogramsInfo-method | Class 'mzR' and sub-classes
class:mzR | Class 'mzR' and sub-classes
class:mzRident | Class 'mzR' and sub-classes
class:mzRnetCDF | Class 'mzR' and sub-classes
class:mzRpwiz | Class 'mzR' and sub-classes
class:mzRramp | Class 'mzR' and sub-classes
close | Class 'mzR' and sub-classes
close-method | Class 'mzR' and sub-classes
copyWriteMSData | Write MS spectrum data to a MS file copying metadata from the originating file
database | Access the metadata from an 'mzR' object.
database-method | Class 'mzR' and sub-classes
detector | Access the metadata from an 'mzR' object.
detector-method | Class 'mzR' and sub-classes
enzymes | Access the metadata from an 'mzR' object.
enzymes-method | Class 'mzR' and sub-classes
fileName | Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
fileName-method | Class 'mzR' and sub-classes
get3Dmap | Access the raw data from an 'mzR' object.
get3Dmap-method | Access the raw data from an 'mzR' object.
header | Access the raw data from an 'mzR' object.
header-method | Access the raw data from an 'mzR' object.
initializeRamp | Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
initializeRamp-method | Class 'mzR' and sub-classes
instrumentInfo | Access the metadata from an 'mzR' object.
instrumentInfo-method | Class 'mzR' and sub-classes
ionisation | Access the metadata from an 'mzR' object.
ionisation-method | Class 'mzR' and sub-classes
isInitialized | Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
isInitialized-method | Class 'mzR' and sub-classes
isolationWindow | Returns the ion selection isolation window
isolationWindow-method | Returns the ion selection isolation window
isolationWindow-methods | Returns the ion selection isolation window
length | Class 'mzR' and sub-classes
length-method | Class 'mzR' and sub-classes
manufacturer | Access the metadata from an 'mzR' object.
manufacturer-method | Class 'mzR' and sub-classes
model | Access the metadata from an 'mzR' object.
model-method | Class 'mzR' and sub-classes
modifications | Access the metadata from an 'mzR' object.
modifications-method | Class 'mzR' and sub-classes
mzidInfo | Access the metadata from an 'mzR' object.
mzidInfo-method | Class 'mzR' and sub-classes
mzR | parser for mzXML, mzData, mzML and mzid files (mass spectrometry data)
mzR-class | Class 'mzR' and sub-classes
mzRident-class | Class 'mzR' and sub-classes
mzRnetCDF-class | Class 'mzR' and sub-classes
mzRpwiz-class | Class 'mzR' and sub-classes
mzRramp-class | Class 'mzR' and sub-classes
nChrom | Access the raw data from an 'mzR' object.
openIDfile | Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
openMSfile | Create and check mzR objects from netCDF, mzXML, mzData or mzML files.
para | Access the metadata from an 'mzR' object.
para-method | Class 'mzR' and sub-classes
peaks | Access the raw data from an 'mzR' object.
peaks-method | Access the raw data from an 'mzR' object.
peaksCount | Access the raw data from an 'mzR' object.
peaksCount-method | Access the raw data from an 'mzR' object.
psms | Access the metadata from an 'mzR' object.
psms-method | Class 'mzR' and sub-classes
pwiz.version | Get the version number of pwiz backend.
runInfo | Access the metadata from an 'mzR' object.
runInfo-method | Class 'mzR' and sub-classes
sampleInfo | Access the metadata from an 'mzR' object.
sampleInfo-method | Class 'mzR' and sub-classes
score | Access the metadata from an 'mzR' object.
score-method | Class 'mzR' and sub-classes
softwareInfo | Access the metadata from an 'mzR' object.
softwareInfo-method | Class 'mzR' and sub-classes
sourceInfo | Access the metadata from an 'mzR' object.
sourceInfo-method | Class 'mzR' and sub-classes
specParams | Access the metadata from an 'mzR' object.
specParams-method | Class 'mzR' and sub-classes
spectra | Access the raw data from an 'mzR' object.
spectra-method | Access the raw data from an 'mzR' object.
substitutions | Access the metadata from an 'mzR' object.
substitutions-method | Class 'mzR' and sub-classes
tic | Access the raw data from an 'mzR' object.
tic-method | Access the raw data from an 'mzR' object.
tolerance | Access the metadata from an 'mzR' object.
tolerance-method | Class 'mzR' and sub-classes
writeMSData | Write MS spectrum data to an MS file
writeMSData-method | Write MS spectrum data to an MS file