Drop defunct susie_rss flags; add --rss-control to rss_analysis - #1396
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susieR 0.16.6 moved R_mismatch_method / check_prior into susie_rss_control(), so setting the old --r-mismatch-method / --check-prior flags errors. Remove them from fine_mapping.R and rss_analysis.ipynb, document --r-mismatch eb_mix, and add a --rss-control JSON flag (+ rss_control notebook param) that forwards susie_rss_control() settings via pecotmr's fineMappingPipeline(rssControl=). Requires susieR >= 0.16.6 for eb_mix / rss_control; default runs unchanged.
…b_mix susieR 0.16.6 moved R_mismatch_method / check_prior into susie_rss_control(), so the old --r-mismatch-method / --check-prior flags error. Remove them from fine_mapping.R and rss_analysis.ipynb, add a --rss-control JSON flag (+ rss_control notebook param) forwarding susie_rss_control() settings via fineMappingPipeline(rssControl=), and make eb_mix the default LD-mismatch correction (was eb). Requires susieR >= 0.16.6. Default-run results shift from eb to eb_mix.
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What
susieR 0.16.6 moved
R_mismatch_method/check_priorintosusie_rss_control().fine_mapping.R— remove--r-mismatch-method/--check-prior;--r-mismatchdocumentsnone | eb | eb_mix; add--rss-control(JSON →fineMappingPipeline(rssControl=), pecotmr's susie_rss_control() passthrough; non-object JSON errors).rss_analysis.ipynb— drop the two params; add anrss_controlparam forwarded as--rss-controlwhen set; documenteb_mix+ susieR >= 0.16.6.Depends on
pecotmr #557 (merged) — the fit path ignores the old args and exposes
rssControl; runtime needs susieR >= 0.16.6.Testing
Merged pecotmr
main(#557+#558) + susieR 0.16.6, real chr21 AD_Bellenguez:sos runwith--r-mismatch eb_mix --rss-control '{"check_prior":true,"mismatch_estimator":"map"}'completes all steps.fine_mapping.R: valid--rss-controlcompletes; non-JSON errors; removed flags absent from--help.