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Implement rawRR backend to read data from raw files #186

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hechth opened this issue Mar 30, 2023 · 0 comments
Open
6 tasks

Implement rawRR backend to read data from raw files #186

hechth opened this issue Mar 30, 2023 · 0 comments
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enhancement New feature or request good first issue Good for newcomers

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@hechth
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hechth commented Mar 30, 2023

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.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
@hechth hechth added enhancement New feature or request good first issue Good for newcomers labels Apr 18, 2024
@wverastegui wverastegui self-assigned this Apr 24, 2024
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