xcmsRaw {xcms}R Documentation

Constructor for xcmsRaw objects which reads NetCDF/mzXML files

Description

This function handles the task of reading a NetCDF/mzXML file containing LC/MS or GC/MS data into a new xcmsRaw object. It also transforms the data into profile (maxrix) mode for efficient plotting and data exploration.

Usage

xcmsRaw(filename, profstep = 1, profmethod = "intlin", profparam = list())

Arguments

filename path name of the NetCDF or mzXML file to read
profstep step size (in m/z) to use for profile generation
profmethod method to use for profile generation
profparam extra parameters to use for profile generation

Details

If profstep is set to 0, no profile matrix is generated. Only first level MS data is read, not MS/MS, etc.)

Value

A xcmsRaw object.

Note

Author(s)

Colin A. Smith, csmith@scripps.edu

References

NetCDF file format: http://my.unidata.ucar.edu/content/software/netcdf/

mzXML file format: http://sashimi.sourceforge.net/software_glossolalia.html

See Also

xcmsRaw-class, profStep, profMethod


[Package xcms version 1.4.0 Index]