README.md

In rformassspectrometry/MsBackendTimsTof: Mass spectrometry Data Backend for Bruker TimsTOF Files

MsBackendTimsTof

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

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

rformassspectrometry/MsBackendTimsTof documentation built on Oct. 21, 2023, 4:19 p.m.