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sldsc_enrichment: fix snp-list mode + meta_subset tau_star handling #1319

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Merged
gaow merged 2 commits into from
May 10, 2026
Merged

sldsc_enrichment: fix snp-list mode + meta_subset tau_star handling #1319

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d89e391
sldsc_enrichment: normalize annot dataframe for ldsc.py --print-snps …
al4225 May 8, 2026
c08438d
sldsc_enrichment [meta_subset]: split tau_star into single/joint via …
al4225 May 8, 2026
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36 changes: 33 additions & 3 deletions code/enrichment/sldsc_enrichment.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -836,12 +836,36 @@
"\n",
" emit_single_local <- ${\"TRUE\" if emit_single else \"FALSE\"}\n",
" emit_joint_local <- ${\"TRUE\" if emit_joint else \"FALSE\"}\n",
" use_print_snps_local <- ${\"TRUE\" if use_print_snps else \"FALSE\"}\n",
" bfile_prefix <- \"${_input[-1]:na}\"\n",
"\n",
" # Reshape annot to match .bim panel for ldsc.py --l2 --print-snps\n",
" # (drop A1/A2/MAF, expand to .bim rows filling 0, take CM from .bim).\n",
" normalize_for_ldsc <- function(df) {\n",
" if (!use_print_snps_local) return(df)\n",
" df <- df[, !names(df) %in% c(\"A1\", \"A2\", \"MAF\", \"CM\"), drop = FALSE]\n",
" annot_cols <- setdiff(names(df), c(\"CHR\", \"BP\", \"SNP\"))\n",
" bim <- as.data.frame(fread(paste0(bfile_prefix, \".bim\"), header = FALSE,\n",
" col.names = c(\"CHR\", \"SNP\", \"CM\", \"BP\", \"A1\", \"A2\")))\n",
" bim$CHR <- as.character(bim$CHR); df$CHR <- as.character(df$CHR)\n",
" idx <- match(bim$SNP, df$SNP)\n",
" out <- data.frame(CHR = bim$CHR, BP = bim$BP, SNP = bim$SNP, CM = bim$CM,\n",
" stringsAsFactors = FALSE)\n",
" for (col in annot_cols) {\n",
" v <- rep(0, nrow(bim))\n",
" non_na <- !is.na(idx)\n",
" v[non_na] <- df[[col]][idx[non_na]]\n",
" out[[col]] <- v\n",
" }\n",
" out\n",
" }\n",
"\n",
" # ---- Write N single-target .annot files (when requested) ----\n",
" if (emit_single_local) {\n",
" for (i in seq_len(N_local)) {\n",
" out_anno <- ref_anno\n",
" out_anno$ANNOT <- score_list[[i]]\n",
" out_anno <- normalize_for_ldsc(out_anno)\n",
" name <- paste0(\"${annotation_name}\", \"_single_\", i)\n",
" out_path_gz <- file.path(\"${cwd:a}\", name, paste0(name, \".${input_chroms[_index]}.annot.gz\"))\n",
" out_path_tsv <- sub(\"\\\\.gz$\", \"\", out_path_gz)\n",
Expand All @@ -856,6 +880,7 @@
" for (i in seq_len(N_local)) {\n",
" joint_anno[[paste0(\"ANNOT_\", i)]] <- score_list[[i]]\n",
" }\n",
" joint_anno <- normalize_for_ldsc(joint_anno)\n",
" joint_name <- paste0(\"${annotation_name}\", \"_joint\")\n",
" joint_out_gz <- file.path(\"${cwd:a}\", joint_name, paste0(joint_name, \".${input_chroms[_index]}.annot.gz\"))\n",
" joint_out_tsv <- sub(\"\\\\.gz$\", \"\", joint_out_gz)\n",
Expand Down Expand Up @@ -1231,10 +1256,15 @@
"\n",
" subset_per_trait <- res$per_trait[subset_traits]\n",
"\n",
" # Map wide names (tau_star_single/joint) to bare names meta_sldsc_random expects.\n",
" view_single <- pecotmr:::.sldsc_view_for_meta(subset_per_trait, \"single\")\n",
" view_joint <- pecotmr:::.sldsc_view_for_meta(subset_per_trait, \"joint\")\n",
"\n",
" out <- list(\n",
" tau_star = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"tau_star\")), target_cats),\n",
" enrichment = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"enrichment\")), target_cats),\n",
" enrichstat = setNames(lapply(target_cats, function(c) meta_sldsc_random(subset_per_trait, c, \"enrichstat\")), target_cats)\n",
" tau_star_single = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"tau_star\")), target_cats),\n",
" tau_star_joint = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_joint, c, \"tau_star\")), target_cats),\n",
" enrichment = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"enrichment\")), target_cats),\n",
" enrichstat = setNames(lapply(target_cats, function(c) meta_sldsc_random(view_single, c, \"enrichstat\")), target_cats)\n",
" )\n",
"\n",
" saveRDS(out, \"${_output[0]}\")\n",
Expand Down