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Updates #19

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2 changes: 1 addition & 1 deletion fine-mapping/finemapping_results_wrangler.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -325,8 +325,8 @@
" idx = 0\n",
" for (f in files) {\n",
" idx = idx + 1\n",
" rds_file = dscrutils::read_dsc(f)\n",
" unit = dirname(f)\n",
" rds_file = dscrutils::dscread(unit, tools::file_path_sans_ext(basename(f)))\n",
" processed_dat[[idx]] = get_${source}_output(unit, rds_file)\n",
" cat(\"We are at unit #\", idx, \":\", unit, \"\\n\")\n",
" }\n",
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2 changes: 1 addition & 1 deletion fine-mapping/summary_statistics_finemapping.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -376,7 +376,7 @@
" }\n",
" library(susieR)\n",
" L = min(${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.

" prior_weights=prior, track_fit=${\"T\" if track_fit else \"F\"})\n",
" s$prior = prior\n",
" s$z = z_scores\n",
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