Question: how to import a CDF file in R ?
0
gravatar for Nemo
4.0 years ago by
Nemo80
India
Nemo80 wrote:

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 

 

xcms R metams mseasy • 1.9k views
ADD COMMENTlink modified 4.0 years ago by peer.karmaus0 • written 4.0 years ago by Nemo80
Answer: how to import a CDF file in R ?
0
gravatar for Bernd Fischer
4.0 years ago by
Bernd Fischer540
Germany / Heidelberg / DKFZ
Bernd Fischer540 wrote:

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.

 

ADD COMMENTlink written 4.0 years ago by Bernd Fischer540

@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 .

ADD REPLYlink written 4.0 years ago by Nemo80
Answer: how to import a CDF file in R ?
0
gravatar for peer.karmaus
4.0 years ago by
United States
peer.karmaus0 wrote:

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

ADD COMMENTlink written 4.0 years ago by peer.karmaus0
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