compute_snpQ2: compute_snpQ2

compute_snpQ2R Documentation

compute_snpQ2

Description

Compute SNP-specific Q2 by averaging over all pairs of samples

Usage

.compute_snpQ2(refcount, totcount, pairs, verbose)

Arguments

refcount

Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele

totcount

Matrix of nsnpxnpop with total counts or read coverages

pairs

Matrix of npoppairsx2 giving the index for all the pairs of pops included in the computation

verbose

Logical (if TRUE progression bar is printed on the terminal)

Details

Compute all the SNP-specific Q2 over all pop. pairs (useful for Fst computation with method Identity).

Value

Return a vector of length nsnps with SNP-specific Q2

Examples

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poolfstat documentation built on April 4, 2025, 1:49 a.m.