compute_F3fromF2

.compute_F3fromF2

Compute all F3 from overall F2 values

Functions for the computation of f- and D-statistics (estimation of 'Fst', 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' or 'SelEstim' format).

Mathieu Gautier

poolfstat

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

compute_F3fromF2 function

<dl><dt>F2val</dt>
<dd>Numeric vector of length nF2=(npop*(npop-1))/2 with all pairwise F2 estimates</dd>
<dt>Hval</dt>
<dd>Numeric vector of length npop with all within pop heterozygosity estimates</dd>
<dt>npops</dt>
<dd>Integer giving the number of populations</dd></dl>

Arguments

compute_F3fromF2 — compute_F3fromF2

<dl>

<dt>F2val</dt>
<dd>Numeric vector of length nF2=(npop*(npop-1))/2 with all pairwise F2 estimates</dd>


<dt>Hval</dt>
<dd>Numeric vector of length npop with all within pop heterozygosity estimates</dd>


<dt>npops</dt>
<dd>Integer giving the number of populations</dd>

</dl>

compute_F3fromF2: compute_F3fromF2

Description

Usage

Value

Arguments

Details

Examples