compute_blockDdenom: compute_blockDdenom

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

compute_blockDdenom

Description

Compute the denominator of the Dstat for all quadruplet configuration and each block-jackknife block (if any) and overall SNPs (within or outside blocks)

Usage

.compute_blockDdenom(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 the denominator of the Dstat for all quadruplet configuration and each block-jackknife block (if any) and overall SNPs (within or outside blocks)

Value

Return a matrix with nf4=(npops*(npops-1)/2)*((npops-2)*(npops-3)/2)/2 rows and nblocks+1 columns giving the mean Dstat-denominator (1-Q2ab)(1-Q2cd) for all quadruplet configuration and within each block-jackknife sample and over all SNPs (last column)

Examples

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