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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)
The text was updated successfully, but these errors were encountered:
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:
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).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
)The text was updated successfully, but these errors were encountered: