compute_H1: compute_H1

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

compute_H1

Description

Compute (uncorrected) 1-Q1 for each block-jackknife block (if any) and over all the SNPs (i.e., either within or outside blocks)

Usage

.compute_H1(refcount, totcount, nblocks, block_id, 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
nblocks	Integer giving the number of block-jackknife blocs (may be 0 if no block-jackknife)
block_id	Integer vector of length nsnps with the (0-indexed) id of the block to which each SNP belongs (-1 for SNPs outside blocks)
verbose	Logical (if TRUE progression bar is printed on the terminal)

Details

Compute all the (uncorrected) H1=1-Q1 for each block-jackknife block (if any) and overall SNPs (within or outside blocks). It is indeed more convenient to compute H1 (rather than Q1) to apply corrections afterwards within R function

Value

Return a matrix with npops rows and nblocks+1 column giving the mean H1 of each pop within each block and for all SNPs (last column)

Examples

#

poolfstat documentation built on Sept. 8, 2023, 5:49 p.m.