pgenlibr (version 0.4.0)

GetAlleleCt: 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)

Value

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

Arguments

pvar_or_pgen

Object returned by NewPvar() or NewPgen().

variant_num

Variant index (1-based).