Compute SNP-specific Q2 by averaging over all pairs of samples using weighting averages of pairwise Q2 (eq. A47 in Hivert et al., 2018)
.compute_snpQ2rw(refcount, totcount, pairs, sampsize, readcount, verbose)Return a vector of length nsnps with SNP-specific Q2
Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele
Matrix of nsnpxnpop with total counts or read coverages
Matrix of npoppairsx2 giving the index for all the pairs of pops included in the computation
Vector of length npop giving the haploid sample size (not used for count data)
Logical (if TRUE PoolSeq data assumed i.e. weights depending on haploid size, otherwise weights depend on total counts)
Logical (if TRUE progression bar is printed on the terminal)
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).