compute_snpFstAov: compute_snpFstAov

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

compute_snpFstAov

Description

Compute SNP-specific MSG, MSP and nc used to derived the Anova estimator of Fst for allele count or read count data (Pool-Seq)

Usage

.compute_snpFstAov(refcount, totcount, hapsize, 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
hapsize	Vector of length npop giving the haploid size of each pool (if one element <=0, counts are interpreted as count data)
verbose	Logical (if TRUE progression bar is printed on the terminal)

Details

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

Value

Return a nsnpsx3 matrix with SNP-specific MSG, MSP and nc

Examples

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