sldsc_enrichment: document snplist vs no-snplist path; add --target-categories-label; fix MWE#1322
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…x MWE
- [make_annotation_files_ldscore]: explain --snp_list -> ldsc.py --l2 --print-snps
(output .l2.ldscore.gz) vs no --snp_list -> compute_ldscores.py (.l2.ldscore.parquet);
document the root cause of "L2_0" vs "ANNOT_0" in .results (ldsc.py hard-codes the
LD-score column name to "L2" when n_annot == 1, dropping the annot's original column
name; compute_ldscores.py always keeps it); note the CM-column requirement for
--snp_list (ldsc.py --l2 --print-snps needs CM and .bim-aligned annot; handled by
normalize_for_ldsc; .bim must carry cM positions when using --ld-wind-cm).
- [get_heritability]: document the ".results" Category "_0 / _1" suffix = position of
the LD-score source in --ref-ld-chr (target = 0, baseline = 1), incl. joint-dir cases.
- MWE markdown ("1.2 joint tau"): explain --snp_list is optional and orthogonal to
single/joint, does not change LD-score values, and downstream commands are unchanged.
- MWE postprocess cell: fix path inconsistencies (output/polyfun/heritability ->
output/heritability; output/polyfun/ldscores/my_analysis_joint -> output/my_analysis_joint);
replace placeholder "--target-categories anno1 anno2" with the real names
(ANNOT_1_0 ANNOT_2_0) + a note on where they come from / that auto-detect works.
- get_heritability & postprocess MWE: add "allm variant: --maf-cutoff 0" comment.
- [global]: remove the dead, never-wired `Mref` parameter (M_ref is auto-computed from
the .frq files by compute_sldsc_M_ref).
Doc/MWE only — no workflow logic changed.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…endly target names Pass-through for pecotmr::sldsc_postprocessing_pipeline(..., target_labels=). When --target-categories-label is given (same order as --target-categories), the "target" column / tau*-block column names in the output RDS are renamed to those labels (params$target_categories holds the labels, params$target_categories_orig the original polyfun .results names). Omit it to keep the original names — no behaviour change otherwise. Updated the postprocess MWE, header, and the [meta_subset] note (the cached RDS already carries the labels). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Documentation + small interface additions to
code/enrichment/sldsc_enrichment.ipynb(pairs with StatFunGen/pecotmr#489).Documentation
[make_annotation_files_ldscore]— explain the snplist vs no-snplist split:--snp_listroutes toldsc.py --l2 --print-snps(output.l2.ldscore.gz), absent routes tocompute_ldscores.py(output.l2.ldscore.parquet). Root cause of theL2_0vsANNOT_0.resultsCategory name:ldsc.pyhard-codes the LD-score column to"L2"when there is exactly one annotation (dropping the annot's column name), whilecompute_ldscores.pyalways keeps it. Also note the snplist-only requirement that the target annot carry aCMcolumn and line up row-for-row with the plink.bim.[get_heritability]— explain the.resultsCategory_0/_1suffix: each polyfun call gets exactly two--ref-ld-chrsources (target = index 0, baseline = index 1), so target annots come out asANNOT_0/L2_0/ANNOT_1_0… and baseline asbase_1,Coding_UCSC_1, …--target-categories(if passed explicitly) must match this exactly.[postprocess]/ section 3 markdown — document the new--target-categories-label.Interface
[postprocess]— new--target-categories-labelparameter (same order as--target-categories), passed through topecotmr::sldsc_postprocessing_pipeline(target_labels=). Renames thetargetcolumns /tau*-block names in the output RDS to friendly names (e.g.ANNOT_1_0 ANNOT_2_0→quantile_eQTL eQTL); originals kept inparams$target_categories_orig. Omit to keep the polyfun.resultsnames — unchanged default behaviour.parameter: Mref = -1from[global](no longer read by anything).MWE fixes
output/heritability,output/my_analysis_joint), changed the illustrative--target-categories anno1 anno2to real.resultsCategory names (ANNOT_1_0 ANNOT_2_0), added anallmnote (--maf-cutoff 0).Testing
Ran the last steps of the
updated_pipeline_by_gao/testMWE (postprocess+meta_subset) against this notebook + the pecotmr PR branch, with and without--target-categories-label: relabel works (params$target_categories = quantile_eQTL,target_categories_orig = ANNOT_0,meta_subsetinherits the label), default path unchanged, numeric values identical between the two.🤖 Generated with Claude Code