Contents
generate$sources
GWAS sources
generate$sources declares where GWAS summary statistics come from:
generate$sources$opengwas,
generate$sources$gwascatalog and
generate$sources$local. Each returns a ResourceSpecSet of
unresolved gwas.sumstats specifications to pass to generate$models(sources = ).
Nothing is fetched until execution.
Extending PolyGenius
A new source is a Rule that produces gwas.sumstats, plus a spec constructor in
generate.sources.*. It must honour the contract of the existing three: a variant table
with chr, position, ea, nea, beta and pval, a normalised build label,
rows without a usable coordinate dropped and counted, and ncase/ncontrol emitted
when known. See
Extending PolyGenius
and ask the generate-architect agent.
See Also
Other generate-sources:
generate-gwascatalog,
generate-local,
generate-opengwas