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Nov 17, 2020
| " library(susieR)\n", | ||
| " L = min(${L}, length(z_scores))\n", | ||
| " s = susie_z(z_scores, r, r_tol = 5e-3, L = L, min_abs_corr = 0.1,\n", | ||
| " s = susie_rss(z_scores, r, r_tol = 5e-3, L = L, min_abs_corr = 0.1,\n", |
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@sq-96 z_ld_weight is a crucial parameter that hsould be included. You probably have to pass in an additional parameter "ref_panel_size" . Otherwise the result may not be reliable as shown in the warning message of your data. See also this section https://stephenslab.github.io/susieR/articles/finemapping_summary_statistics.html#using-ld-from-reference-panel for before and after using the parameter.
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Changes in summary_statistics_finemapping.ipynb:
s = susie_rss(z_scores, r, r_tol = 5e-3, L = L, min_abs_corr = 0.1, prior_weights=prior, track_fit=${"T" if track_fit else "F"})
Changes in finemapping_results_wrangler.ipynb
unit = dirname(f)
rds_file = dscrutils::dscread(unit, tools::file_path_sans_ext(basename(f)))