compute_snpQ2 | R Documentation |
Compute SNP-specific Q2 by averaging over all pairs of samples
.compute_snpQ2(refcount, totcount, pairs, verbose)
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) |
Compute all the SNP-specific Q2 over all pop. pairs (useful for Fst computation with method Identity).
Return a vector of length nsnps with SNP-specific Q2
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