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Single variant single trait runs fail to generate QQplot #199

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roskamsh opened this issue Nov 5, 2024 · 1 comment · Fixed by #200
Closed

Single variant single trait runs fail to generate QQplot #199

roskamsh opened this issue Nov 5, 2024 · 1 comment · Fixed by #200

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@roskamsh
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roskamsh commented Nov 5, 2024

Upon running the targene-pipeline (v0.11.0) using a single variant and single trait, the final step GenerateOutputs() fails. Upon further inspection, this only occurs when the number of non-NA P-values per-estimator is 1. This would occur when you are running TarGene with only a single variant and single trait (currently experiencing this when reproducing FTO variant on BMI results on the AoU cohort).

Suggested changes:

  • Make QQplot generation optional when only a single p-value (per-estimator) is present.
  • Update targene-pipeline to make this output QQplot.png optional.
@roskamsh roskamsh linked a pull request Nov 5, 2024 that will close this issue
@olivierlabayle
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What is the reason behind the NA in this case?

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