compute_snpQ2w: compute_snpQ2rw

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

compute_snpQ2rw

Description

Compute SNP-specific Q2 by averaging over all pairs of samples using weighting averages of pairwise Q2 (eq. A47 in Hivert et al., 2018)

Usage

.compute_snpQ2rw(refcount, totcount, pairs, sampsize, readcount, 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
sampsize	Vector of length npop giving the haploid sample size (not used for count data)
readcount	Logical (if TRUE PoolSeq data assumed i.e. weights depending on haploid size, otherwise weights depend on total counts)
verbose	Logical (if TRUE progression bar is printed on the terminal)

Details

Compute SNP-specific Q2 by averaging over all pairs of samples using weighting averages of pairwise Q2 (eq. A47 in Hivert et al., 2018) (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.