Data Model

snputils centers work around lightweight objects that hold data arrays plus the sample, variant, ancestry, phenotype, or segment metadata needed to interpret them.

Core Objects

• snputils.SNPObject stores genotype calls and variant metadata.

• snputils.LocalAncestryObject stores ancestry calls along chromosomes.

• snputils.GlobalAncestryObject stores ADMIXTURE-style ancestry proportions.

• snputils.PhenotypeObject and snputils.MultiPhenotypeObject store trait data.

• snputils.GRGObject stores genotype representation graph data.

• snputils.IBDObject stores identity-by-descent segment tables.

Most objects provide a copy() method, shape/count properties, and filtering helpers that return object-level views or copies instead of loose arrays.

snpobj = su.read_snp("cohort.pgen")
snpobj.n_samples, snpobj.n_snps

Use the API reference when you need exact constructor arguments or property names.