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Update mapping files for ocular phenotypes #78

Merged
merged 6 commits into from
Jun 24, 2024
Merged

Update mapping files for ocular phenotypes #78

merged 6 commits into from
Jun 24, 2024

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marinak-ebi
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Closes #77.

I added a module which takes file from IMPRESS and modifies the mapping files in the pipeline according to it, so that all parameters are included.

I assume that the same parameter value has the same meaning between different centres. For example, I don't have values for RBRCLA_EYE_003_001 as it's a new parameter, but I'm using the same parameter interpretations as for IMPC_EYE_003_001:

  • absent → 0 (normal for the purposes of p-value calculation)
  • present left eye/present right eye/present both eyes → 1 (abnormal for the purposes of p-value calculation)

@marinak-ebi marinak-ebi requested a review from ficolo May 24, 2024 13:50
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🙏🏻 this one is new! Good catch.

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Hopefully we won't need to run this script every release.

@marinak-ebi marinak-ebi merged commit d792f5b into dev Jun 24, 2024
@marinak-ebi marinak-ebi deleted the eye-issue branch June 24, 2024 09:27
@marinak-ebi marinak-ebi self-assigned this Jul 8, 2024
@marinak-ebi marinak-ebi linked an issue Jul 8, 2024 that may be closed by this pull request
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Ocular phenotypes LA data still go through the analysis
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