compute_F3fromF2samples

.compute_F3fromF2samples

Compute all F3 from F2 values obtained from each block-jackknife bloc

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_F3fromF2samples function

<dl><dt>blockF2</dt>
<dd>Numeric Matrix with nF2=(npop*(npop-1))/2 rows and nblocks columns matrix containing pairwise-pop F2 estimates for each block-jackknife sample (l.o.o.)</dd>
<dt>blockHet</dt>
<dd>Numeric Matrix with npop rows and nblocks columns containing all within pop heterozygosity estimates for each block-jackknife sample (l.o.o.)</dd>
<dt>npops</dt>
<dd>Integer giving the number of populations</dd>
<dt>verbose</dt>
<dd>Logical (if TRUE progression bar is printed on the terminal)</dd></dl>

Arguments

compute_F3fromF2samples — compute_F3fromF2samples

<dl>

<dt>blockF2</dt>
<dd>Numeric Matrix with nF2=(npop*(npop-1))/2 rows and nblocks columns matrix containing pairwise-pop F2 estimates for each block-jackknife sample (l.o.o.)</dd>


<dt>blockHet</dt>
<dd>Numeric Matrix with npop rows and nblocks columns containing all within pop heterozygosity estimates for each block-jackknife sample (l.o.o.)</dd>


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


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

</dl>

compute_F3fromF2samples: compute_F3fromF2samples

Description

Usage

Value

Arguments

Details

Examples