compute_snpHierFstAov: compute_snpHierFstAov

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

compute_snpHierFstAov

Description

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

Usage

.compute_snpHierFstAov(refcount, totcount, hapsize, popgrpidx, 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)
popgrpidx	Vector of length npop giving the index (coded from 0 to ngrp-1) of the group of origin
verbose	Logical (if TRUE progression bar is printed on the terminal)

Details

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

Value

Return a nsnpsx6 matrix with SNP-specific MSI, MSP, MSG, nc, nc_p and nc_pp

Examples

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