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ireneisdoomed
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Sep 14, 2026
ireneisdoomed
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Well spotted! I have double checked that the columns with NaN in the numeric columns are: beta, oddsRatio + the correspondent 4 fields about the upper and lower bounds of the confidence intervals.
Because you are standardising the effect and beta columns directly, the derived columns will be fixed too.
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Summary
beta/oddsRatioas SQLNULLwhen no effect size is reported, e.g. most gene_burden rows correctly getdirectionOnTrait: NULLwhen both fields are null.directionOnTrait: 'risk'even though no effect size was ever computed, e.g.beta: NaN,oddsRatio: null."NaN"('BETA Burden'in BRaVa's S14/S15,'effect'/BETAin Genes & Health's ST9/ST13/ST15), which Spark's double cast turns into a floatNaNrather thanNULL.NaNas larger than any other value, sodirection_on_trait_expression'sbeta > 0.0(oroddsRatio > 1.0) evaluatesTRUEfor aNaNinput, misclassifying 5,617 rows as'risk'.Fix
_process_brava_granular, normalise'BETA Burden'fromNaNtoNULLright after casting it to double, so SKAT/SKAT-O rows (which carry no effect size) behave as missing.process_genes_and_health_gene_burden, normalise'effect'fromNaNtoNULLright after unioning the three source tables, before it's used to derivebeta/oddsRatio.beta: null,oddsRatio: null→directionOnTrait: nullinstead of'risk'.