Compute SNP-specific MSG, MSP and nc used to derived the Anova estimator of Fst for allele count or read count data (Pool-Seq)
.compute_snpFstAov(refcount, totcount, hapsize, verbose)Return a nsnpsx3 matrix with SNP-specific MSG, MSP and nc
Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele
Matrix of nsnpxnpop with total counts or read coverages
Vector of length npop giving the haploid size of each pool (if one element <=0, counts are interpreted as count data)
Logical (if TRUE progression bar is printed on the terminal)
Compute SNP-specific Q1 and Q2 based on Anova estimator of Fst for allele count or read count data (Pool-Seq). For allele count data, the implemented estimator corresponds to that described in Weir, 1996 (eq. 5.2) For read (Pool-Seq) data, the implemented estimator corresponds to that described in Hivert et al., 2016