There are many packages avaiable for GC/MS analysis, however, all of them just import data from their own package.
Mz question is that if I have a CDF data saved in the desktop, how can I read it in R?
any comment is appreciated
You can try the package mzR to read in the mass spec data. Depending on the CDF file format, this may be the best way.
Other possibilities to read in netCDF files are the packages rhdf5 or ncdf.
@Bernd Fischer thanks for the comment but none of the above packages had a solution. the data has a cdf format but i dont know the exact structure to retrive info based on ncdf. the rhdf5 is also not working fine for me (at least i could not use it). The mzR is very limited and uses mzXML format .
It might help if you convert your CDF with ProteoWizard to mzXML in centroided mode: https://xcmsonline.scripps.edu/docs/fileformats.html
then use mzR
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