compute_F2_bjmeans

.compute_F2_bjmeans

Compute the the block-jackknife mean of 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_F2_bjmeans function

<dl><dt>snpQ1</dt>
<dd>the nsnp by npop matrix of Q1 estimates</dd>
<dt>snpQ2</dt>
<dd>the nsnp by (npop*(npop-1))/2 matrix of all pairwise Q2 estimates</dd>
<dt>q1_idx</dt>
<dd>the nsnp by 2 matrix with the indexes of the Q1 needed to compute each F2</dd>
<dt>snp_bj_id</dt>
<dd>integer vector of length nsnp giving the block index of each SNP</dd>
<dt>verbose</dt>
<dd>if TRUE progression bar is printed on the terminal</dd></dl>

Arguments

compute_F2_bjmeans — compute_F2_bjmeans

<dl>

<dt>snpQ1</dt>
<dd>the nsnp by npop matrix of Q1 estimates</dd>


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


<dt>q1_idx</dt>
<dd>the nsnp by 2 matrix with the indexes of the Q1 needed to compute each F2</dd>


<dt>snp_bj_id</dt>
<dd>integer vector of length nsnp giving the block index of each SNP</dd>


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

</dl>

compute_F2_bjmeans: compute_F2_bjmeans

Description

Usage

Value

Arguments

Details

Examples