Carry study-level n_sample through rss_analysis - #1395
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gwas_rss_manifest.R reads an optional n_sample column from --gwas-meta and emits it in the manifest; gwas_sumstats_construct.R adds --n-sample -> GwasSumStats(nSample=) via loadGwasSumStatsFromManifest; rss_analysis.ipynb forwards it when present. Lets a study reporting only a study-level total N (or study-level case/control) be fine-mapped without per-variant N.
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What
Study-level total N (
n_sample) plumbing for the RSS pipeline:gwas_rss_manifest.R— reads an optionaln_samplecolumn from--gwas-meta, carries it into the manifest.gwas_sumstats_construct.R— new--n-sampleflag → the loader manifest →GwasSumStats(nSample=).rss_analysis.ipynb— forwardsn_sampleto--n-samplewhen present (guarded liken_case/n_control).Entry construction from study scalars lives in pecotmr's
loadGwasSumStatsFromManifest, so this side is thin plumbing.Depends on
pecotmr
rss-study-n(thenSampleslot + resolution + the loader's study-scalar entry build).Testing
Against both open pecotmr PRs merged + susieR 0.16.6, real chr21 AD_Bellenguez:
construct.Rend-to-end: studyn_sample→N=study-n(487511); study c/c→effective(292500); per-variant→effective(283145); no N source→errors.generate_manifestscript.sos runwas blocked by a host r-base/r-pecotmr toolchain mismatch unrelated to this change; the generated step scripts run correctly under the r-pecotmr R.)