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.