find_indelneighbor_idx

.find_indelneighbor_idx

Search for the closest indels of the markers

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

find_indelneighbor_idx function

<dl><dt>contig</dt>
<dd>a character string vector corresponding to the CHR field value of the vcf for the markers</dd>
<dt>position</dt>
<dd>an integer vector corresponding to the POSITION value for the markers</dd>
<dt>indels_idx</dt>
<dd>vector of (0-indexed) indices of indels</dd>
<dt>min_dist</dt>
<dd>same as min.dist.from.indels option in <code>vcf2pooldata</code></dd>
<dt>indels_size</dt>
<dd>size of the indels (associated to indels_idx)</dd></dl>

Arguments

find_indelneighbor_idx — find_indelneighbor_idx

<dl>

<dt>contig</dt>
<dd>a character string vector corresponding to the CHR field value of the vcf for the markers</dd>


<dt>position</dt>
<dd>an integer vector corresponding to the POSITION value for the markers</dd>


<dt>indels_idx</dt>
<dd>vector of (0-indexed) indices of indels</dd>


<dt>min_dist</dt>
<dd>same as min.dist.from.indels option in <code>vcf2pooldata</code></dd>


<dt>indels_size</dt>
<dd>size of the indels (associated to indels_idx)</dd>

</dl>

find_indelneighbor_idx: find_indelneighbor_idx

Description

Usage

Value

Arguments

Details

Examples