compute_snpQ2

.compute_snpQ2

Compute SNP-specific Q2 by averaging over all pairs of samples

Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in TreeMix, BayPass and SelEstim format).

Mathieu Gautier

poolfstat

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

compute_snpQ2 function

<dl><dt>refcount</dt>
<dd>Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele</dd>
<dt>totcount</dt>
<dd>Matrix of nsnpxnpop with total counts or read coverages</dd>
<dt>pairs</dt>
<dd>Matrix of npoppairsx2 giving the index for all the pairs of pops included in the computation</dd>
<dt>verbose</dt>
<dd>Logical (if TRUE progression bar is printed on the terminal)</dd></dl>

Arguments

compute_snpQ2 — compute_snpQ2

<dl>

<dt>refcount</dt>
<dd>Matrix of nsnpxnpop with counts (genotype or reads) for the reference allele</dd>


<dt>totcount</dt>
<dd>Matrix of nsnpxnpop with total counts or read coverages</dd>


<dt>pairs</dt>
<dd>Matrix of npoppairsx2 giving the index for all the pairs of pops included in the computation</dd>


<dt>verbose</dt>
<dd>Logical (if TRUE progression bar is printed on the terminal)</dd>

</dl>

compute_snpQ2: compute_snpQ2

Description

Usage

Value

Arguments

Details

Examples