search

lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics
http://lgatto.github.io/MSnbase/
123 stars 50 forks source link

readMSData function on mzXML file format #576

Closed Marievlm closed 2 years ago

Marievlm commented 2 years ago

Hello Laurent,

Thank you for your great package MSnbase.

Since the last version of MSnbase, I'm not able to load my mzXML file by the function readMSData. The error after executing the function is : Error in FUN(X[[i]], ...) : inherits(x, "mzR") is not TRUE

I have checked if the file exists and it is. It's surprising because it works with mzML format. I have tried with different R versions but I still have the same error.

Thank you in advance for your help.

Marie

Marievlm commented 2 years ago

Ok Laurent, I have found the solution ! I have just to specify the entire local URL by dir().

Marievlm commented 2 years ago

Ok Laurent, I have found the solution ! I have just to specify the entire local URL by dir().

lgatto commented 2 years ago

If you use MSnbase for raw data, I would suggest you take a look at Spectra. It builds on the principles of MSnbase + 30 years of cumulative development experience from the R for Mass Spectrometry team. See also here for a book/tutorial.