Expose maf, skip_regions, skip_analysis_pip_cutoff in rss_analysis#1386
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Expose maf, skip_regions, skip_analysis_pip_cutoff in rss_analysis#1386Yining97 wants to merge 1 commit into
Yining97 wants to merge 1 commit into
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Restores three legacy univariate_rss knobs as first-class rss_analysis parameters, routed to summaryStatsQc(): --maf (mafCutoff, default 0.0025), --skip-regions (skipRegion), and --skip-analysis-pip-cutoff (pipCutoffToSkip, default 0.025). construct.R gains --maf/--skip-region flags and rejects the same keys in --qc-args; the notebook forwards all three. A default run now MAF-filters at 0.0025 and PIP-skips at 0.025, matching the legacy workflow. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Restores three legacy
univariate_rssknobs as first-classrss_analysisparameters, all routed tosummaryStatsQc():--maf(mafCutoff, default 0.0025) — was reachable only via--qc-argsand defaulted to 0 (off).--skip-regions chr:start-end …(skipRegion) — drop variants in given windows.--skip-analysis-pip-cutoff(pipCutoffToSkip, default 0.025) — skip a no-signal region;construct.Ralready had the flag but the notebook didn't forward it.construct.Rgains--maf/--skip-regionand rejects the same keys in--qc-args. A default run now MAF-filters at 0.0025 and PIP-skips at 0.025, matching legacy behavior.Validated on the protocol_example chr22 MWE: default filter 24→19 variants;
--maf 0→24; skip-region 19→11;--skip-analysis-pip-cutoff 0.999skips the region; clash guard errors. Full 4-step run green.