GetAlleleCt: Returns the effective number of alleles for a variant. Note...

In pgenlibr: PLINK 2 Binary (.pgen) Reader

Returns the effective number of alleles for a variant. Note that if no pvar was provided to the NewPgen() call, this function may return 2 even at multiallelic variants, since the .pgen may not store allele-count information.

Description

Returns the effective number of alleles for a variant. Note that if no pvar was provided to the NewPgen() call, this function may return 2 even at multiallelic variants, since the .pgen may not store allele-count information.

Usage

GetAlleleCt(pvar_or_pgen, variant_num)

Arguments

pvar_or_pgen	Object returned by NewPvar() or NewPgen().
variant_num	Variant index (1-based).

Value

max(2, <number of alleles the variant_numth variant is known to have>). Note that if no

pgenlibr documentation built on April 3, 2025, 6:21 p.m.