Spectra backend supporting TimsTOF data files via the opentimsr package which bases on the OpenTIMS C++ library. To allow extraction of all spectra and peaks variables the C++ library from Bruker is required, which can be installed using opentimsr::download_bruker_proprietary_code(<local folder>) with <local folder> being the directory to which it should be downloaded).
It is suggested to keep this library in a local folder and to define an environment variable called TIMSTOF_LIB that defines the full path where this file is located (i.e. a character string defining the full file path with the file name). This variable can either be defined system wide, or within the .Rprofile file. An example entry in a .Rprofile could for example be:
options(TIMSTOF_LIB = "/home/jo/lib/libtimsdata.so")
For more information see the package homepage.
Note: currently opentimsr is no longer available on CRAN and needs to be installed from github:
install_github("michalsta/opentims", subdir="opentimsr")
Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.
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