bio-causal-genomics-fine-mapping skillA
bio-causal-genomics-fine-mapping is agent-read markdown (skill) from pku-yuangroup/openai4s: Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or .
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What the file says
## Version Compatibility
Reference examples tested with: susieR 0.12.27+, coloc 5.2.3+, FINEMAP 1.4.2+, PolyFun (head of `omerwe/polyfun` 2024), PAINTOR V3.0, SuSiEx (head of `getian107/SuSiEx`), DAP-G (head of `xqwen/dap`), pyfocus 0.8+, R 4.3+, PLINK 1.9 / 2.0.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('susieR')` then `?susie_rss` to confirm argument names (e.g., `prior_weights` vs `prior_variance` semantics)
- CLI: `finemap --help`, `SuSiEx --help`, `PAINTOR --help`, `dap-g --help` to confirm flags
- Python: `polyfun.py --help`
If a call throws an error about an argument that no longer exists, introspect the installed function and adapt rather than retrying.
# Fine-Mapping
**"Narrow my GWAS locus to the variants likely to be causal"** -> Fit a sparse Bayesian regression that propagates LD into posterior inclusion probabilities (PIPs) and credible sets, then validate that credible sets correspond to physically reasonable haplotypes given the LD reference.
- R (summary statistics + LD): `susieR::susie_rss(z, R, n, L=10)` + `estimate_s_rss` LD diagnostic
- R (individual-level genotypes): `susieR::susie(X, y, L=10)`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-fine-mapping@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-fine-mapping@sha256:1551a62969ba59b2Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_kdmgkyhcnlernsp5)
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Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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