Derive Wald z from beta/se when z is absent - #559
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.resolveSumstatCols now requires a z column OR beta+se: when z is absent but beta and se are present it sets Z = beta/se (the Wald z-score, matching susie_rss z_method=wald). A supplied z takes precedence and is never overwritten; it still errors when neither is available. Lets beta/se-only GWAS sumstats run without a precomputed z (the protocol construct step delegates reading to this loader, so no protocol change is needed).
The .fmFitSusieRss rssControl-forwarding test mocks susie_rss_control(), which only exists in susieR >= 0.16.6; on the CI r44 env (susieR 0.16.4) local_mocked_bindings() can't find the binding and errors. Skip it when susieR lacks susie_rss_control - rssControl is a 0.16.6-only feature anyway. (Test came in with StatFunGen#557; it also fails CI here on this branch.)
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What
Many case/control GWAS publish
beta+sewith noz. The shared sumstats reader.resolveSumstatColsrequiredz, so those inputs errored and had to be pre-processed.Now it requires
zor (beta+se): whenzis absent it derivesZ = beta/se(the Wald z, matchingsusie_rss'sz_method="wald"). A suppliedztakes precedence; it errors only when neither is available.beta/sestill attach as optional columns.Pure pecotmr change — the protocol's
gwas_sumstats_construct.Rdelegates reading toloadGwasSumStatsFromManifest, andbeta/seare already mappable, so no protocol change is needed.Testing
Against
main(post-#557/#558) + susieR 0.16.6, real chr21 AD_Bellenguez:.resolveSumstatCols.Z=beta/se(max err 1.7e-14), QC completes;zpresent →zused, not beta/se (precedence).sos runon a beta/se-only input completes end-to-end.