GitHub - rformassspectrometry/MsBackendTimsTof: Spectra backend supporting TimsTOF data files using the opentimsr package. (original) (raw)

MsBackendTimsTof

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc codecov license

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 usingopentimsr::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 packagehomepage.

Note: currently opentimsr is no longer available on CRAN and needs to be installed from github:

install_github("michalsta/opentims", subdir="opentimsr")

Contributions

Contributions are highly welcome and should follow the contribution guidelines. Also, please check the coding style guidelines in the RforMassSpectrometry vignette.