compute_snpQ1rw: compute_snpQ1rw

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

compute_snpQ1rw

Description

Compute SNP-specific Q1 over all samples using weighting averages of pop. Q1 (eq. A46 in Hivert et al., 2018)

Usage

.compute_snpQ1rw(refcount, totcount, weight, sampsize, readcount, 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
weight	Vector of length npop giving the weighting scheme (w=1 for allele count data and w=poolsize/(poolsize-1) for PoolSeq data)
sampsize	Vector of length npop giving the haploid sample size (not used for count data)
readcount	Logical (if TRUE PoolSeq data assumed i.e. weights depending on haploid size, otherwise weights depend on total counts)
verbose	Logical (if TRUE progression bar is printed on the terminal)

Details

Compute all the SNP-specific Q1 over all pop. samples using weighting averages of pop. Q1 as in eq. A46 of Hivert et al., 2018 (useful for Fst computation with method Identity).

Value

Return a vector of length nsnps with SNP-specific Q1

Examples

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