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Update quantile QTL and qTWAS weight pipeline with new screening parameters #1305

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gaow merged 1 commit into from
Mar 31, 2026
Merged

Update quantile QTL and qTWAS weight pipeline with new screening parameters #1305

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34 changes: 22 additions & 12 deletions code/association_scan/quantile_models/qr_and_twas.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@
"\n",
"\n",
"\n",
"Additionally, the matrix of quantile TWAS weights and pseudo R-squares is calculated and saved using Koenker and Machado's Pseudo R\u00b2 method, as described in their [Koenker and Machado, 1999: Inference in Quantile Regression](https://www.maths.usyd.edu.au/u/jchan/GLM/Koenker&Machado1999InferenceQuantileReg.pdf)"
"Additionally, the matrix of quantile TWAS weights and pseudo R-squares is calculated and saved using Koenker and Machado's Pseudo R² method, as described in their [Koenker and Machado, 1999: Inference in Quantile Regression](https://www.maths.usyd.edu.au/u/jchan/GLM/Koenker&Machado1999InferenceQuantileReg.pdf)"
]
},
{
Expand Down Expand Up @@ -356,13 +356,18 @@
"parameter: indel = True\n",
"parameter: min_twas_maf = 0.01\n",
"parameter: screen_threshold = 0.01\n",
"parameter: qrank_screen_calculate = True\n",
"parameter: marginal_beta_calculate = True\n",
"parameter: twas_weight_calculate = True\n",
"parameter: vqtl_calculate = True\n",
"parameter: screen_method = \"qvalue\"\n",
"parameter: screen_significant = True\n",
"parameter: pre_filter_by_pqr = False\n",
"parameter: initial_corr_filter_cutoff = 0.8\n",
"parameter: full_rank_corr_filter_cutoff = \"seq(0.75, 0.5, by = -0.05)\"\n",
"parameter: ld_reference_meta_file = path()\n",
"# Only focus on a subset of variants\n",
"parameter: keep_variants = path()\n",
"parameter: marginal_beta_calculate = True\n",
"parameter: twas_weight_calculate = True\n",
"parameter: qrank_screen_calculate = True\n",
"parameter: vqtl_calculate = True\n",
"# Analysis environment settings\n",
"parameter: container = \"\"\n",
"# For cluster jobs, number commands to run per job\n",
Expand Down Expand Up @@ -716,9 +721,11 @@
" # Multi-column format: filter by context and molecular_trait_object_id\n",
" # For genotype loading: use union of all matching variants across all contexts\n",
" current_region = \"${_meta_info[2]}\"\n",
" original_region_ids = c(${\",\".join([(\"'%s'\" % x) if isinstance(x, str) else \",\".join([\"'%s'\" % i for i in x]) for x in _meta_info[3]])})\n",
" all_region_ids = unique(c(current_region, original_region_ids))\n",
" current_contexts = conditions\n",
" keep_variants_region_data = keep_variants_data[\n",
" keep_variants_data$molecular_trait_object_id == current_region &\n",
" keep_variants_data$molecular_trait_object_id %in% all_region_ids &\n",
" keep_variants_data$context %in% current_contexts, ]\n",
" keep_variants_list = unique(as.character(keep_variants_region_data$variant_id))\n",
" keep_variants_list = keep_variants_list[keep_variants_list != \"\"]\n",
Expand All @@ -727,9 +734,7 @@
" message(paste(length(keep_variants_list), \"variants matched for region\", current_region,\n",
" \"across\", length(current_contexts), \"contexts (per-context filtering enabled)\"))\n",
" if (length(keep_variants_list) == 0) {\n",
" message(\"No matching variants found, proceeding without variant filter\")\n",
" keep_variants_list = NULL\n",
" keep_variants_per_context = FALSE\n",
" message(\"No matching variants found for this region, marginal coef will be skipped for contexts without variants\")\n",
" }\n",
" } else {\n",
" # Fallback: treat first column as variant_id list\n",
Expand Down Expand Up @@ -811,8 +816,8 @@
" current_keep_variants = current_keep_variants[current_keep_variants != \"\"]\n",
" message(paste(length(current_keep_variants), \"variants for context\", ctx_name))\n",
" } else {\n",
" current_keep_variants = NULL\n",
" message(paste(\"No context-specific variants for\", ctx_name, \"- no variant filter applied\"))\n",
" current_keep_variants = character(0)\n",
" message(paste(\"No context-specific variants for\", ctx_name, \"- skipping marginal coef fitting\"))\n",
" }\n",
" }\n",
"\n",
Expand All @@ -826,7 +831,12 @@
" region_id = paste0(colnames(Y_col), \"_\", names(fdat$residual_Y)[r]),\n",
" quantile_qtl_tau_list = seq(0.05, 0.95, by = 0.05),\n",
" quantile_twas_tau_list = seq(0.01, 0.99, by = 0.01),\n",
" screen_method = \"${screen_method}\",\n",
" screen_threshold = ${screen_threshold},\n",
" screen_significant = ${\"TRUE\" if screen_significant else \"FALSE\"},\n",
" pre_filter_by_pqr = ${\"TRUE\" if pre_filter_by_pqr else \"FALSE\"},\n",
" initial_corr_filter_cutoff = ${initial_corr_filter_cutoff},\n",
" full_rank_corr_filter_cutoff = ${full_rank_corr_filter_cutoff},\n",
" keep_variants = current_keep_variants,\n",
" marginal_beta_calculate = ${\"TRUE\" if marginal_beta_calculate else \"FALSE\"},\n",
" twas_weight_calculate = ${\"TRUE\" if twas_weight_calculate else \"FALSE\"},\n",
Expand Down Expand Up @@ -912,4 +922,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}