extract_vscan_counts

.extract_vscan_counts

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_vscan_counts function

<dl><dt>vcf_data</dt>
<dd>a matrix of String containing count information in VarScan format</dd>
<dt>ad_idx</dt>
<dd>the index of the FORMAT AD field</dd>
<dt>rd_idx</dt>
<dd>the index of the FORMAT RD field</dd></dl>

Arguments

extract_vscan_counts — extract_vscan_counts

<dl>

<dt>vcf_data</dt>
<dd>a matrix of String containing count information in VarScan format</dd>


<dt>ad_idx</dt>
<dd>the index of the FORMAT AD field</dd>


<dt>rd_idx</dt>
<dd>the index of the FORMAT RD field</dd>

</dl>

extract_vscan_counts: extract_vscan_counts

Description

Usage

Value

Arguments

Details

Examples