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Finish the pipeline: Add pickedGroupFDR for quantification #164

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picciama opened this issue Dec 8, 2023 · 0 comments · Fixed by #180
Closed

Finish the pipeline: Add pickedGroupFDR for quantification #164

picciama opened this issue Dec 8, 2023 · 0 comments · Fixed by #180
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enhancement New feature or request

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@picciama
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picciama commented Dec 8, 2023

Is your feature request related to a problem? Please describe.

Currently, oktoberfest stops at rescoring. It would be nice to have pickedGroupFDR for quantification.
Also, pickedGroupFDR should write back the output in the same format as MaxQuant, MSFragger and Sage, the currently supported search engines in oktoberfest.

Describe the solution you would like

  • Make quantification an additional boolean flag in the config that starts pickedGroupFDR based quant

  • Make reformat an additional boolean flag in the config that writes output back in search engine specific format

  • add additional key to input dict in config for additional file input from search engine containing quant information

  • alternatively, make quantification an additional job in the high level API. Does this make sense? Since pickedGroupFDR could be run without rescoring maybe or does it always need rescoring prior to quant?

Additional context

@picciama picciama added the enhancement New feature or request label Dec 8, 2023
@picciama picciama added this to the Release version 0.6.0 milestone Jan 29, 2024
@picciama picciama linked a pull request Jan 31, 2024 that will close this issue
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@picciama picciama removed this from the Release version 0.6.0 milestone Jan 31, 2024
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