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Allow the user to choose which p-value is being plotted for aggregation tests #53

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amstilp opened this issue Apr 13, 2022 · 0 comments
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@amstilp
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amstilp commented Apr 13, 2022

I ran into this in a recent analysis. SMMAT aggregation tests return three p-values (SMMAT, burden, and theta), but we were primarily interested in the burden p-value. It would be useful to allow the user to select which p-value should be plotted. I think this would involve the following:

  • Update TopmedPipeline::getAssoc to allow the user to specify which column is the p-value, with defaults set based on the analysis type (as it currently does).
  • Update assoc_plots.R to allow the user to provide a config parameter specifying which p-value column to use (e.g., pval_variable = pval_burden)
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