extract_allele_names

.extract_allele_names

Extract the alleles from the REF and ALT fields

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

extract_allele_names function

<dl><dt>allele_info</dt>
<dd>a character string vector (concatenated REF and ALT field of the vcf)</dd>
<dt>allele_idx</dt>
<dd>Matrix with indexes of the two alleles of interest for the different markers</dd></dl>

Arguments

extract_allele_names — extract_allele_names

<dl>

<dt>allele_info</dt>
<dd>a character string vector (concatenated REF and ALT field of the vcf)</dd>


<dt>allele_idx</dt>
<dd>Matrix with indexes of the two alleles of interest for the different markers</dd>

</dl>

extract_allele_names: extract_allele_names

Description

Usage

Value

Arguments

Details

Examples