A tutorial on how to use rawRR is available here. The function should also be implemented in the load.lcms.R file and should also come with unit tests of course!
Steps
[ ] do the tutorial (using windows subsystems for Linux)
[ ] try reading some of our raw files which we have on SALLY
[ ] Add a RAW file to the umsa-files repo as testdata
[ ] Implement a unit test for RAW files for load.lcms.R
[ ] Add rawRR to suggested packages
[ ] Implement the load.lcms.R function for raw files of the rawRR package is installed using the require function in R
Possible problems
rawRR requires some DLLs and runs on mono, which means it might not work on linux
the package might not be available via conda
the package might not be compatible with other dependencies
Use the rawRR package to implement a backend reading .raw files into aplcms. The package is described here (https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00866) and is available on bioconductor - there is also a package https://github.com/fgcz/MsBackendRawFileReader to read this with spectra, but I'm not sure if this is actually easier than using the rawrr package directly (https://github.com/fgcz/rawrr/).
A tutorial on how to use rawRR is available here. The function should also be implemented in the
load.lcms.Rfile and should also come with unit tests of course!Steps
load.lcms.Rload.lcms.Rfunction for raw files of the rawRR package is installed using therequirefunction in RPossible problems