compute_Ddenom

.compute_Ddenom

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_Ddenom function

<dl><dt>snpQ2</dt>
<dd>the nsnp by (npop*(npop-1))/2 matrix of all pairwise Q2 estimates</dd>
<dt>f2idx</dt>
<dd>a matrix of nDstat by 2 giving the index of the Q2 required to compute the denominator of the different F4</dd>
<dt>verbose</dt>
<dd>if TRUE progression bar is printed on the terminal</dd></dl>

Arguments

compute_Ddenom — compute_Ddenom

<dl>

<dt>snpQ2</dt>
<dd>the nsnp by (npop*(npop-1))/2 matrix of all pairwise Q2 estimates</dd>


<dt>f2idx</dt>
<dd>a matrix of nDstat by 2 giving the index of the Q2 required to compute the denominator of the different F4</dd>


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

</dl>

compute_Ddenom: compute_Ddenom

Description

Usage

Value

Arguments

Details

Examples