compute_snpQ2onepair

.compute_snpQ2onepair

Compute SNP-specific Q2 for a single pair of samples

Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, 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 and SelEstim format).

Mathieu Gautier

poolfstat

Computing f-Statistics and Building Admixture Graphs Based on
Allele Count or Pool-Seq Read Count Data

compute_snpQ2onepair function

<dl><dt>refcount1</dt>
<dd>Vector of count (genotype or reads) for the reference allele in the first sample</dd>
<dt>refcount2</dt>
<dd>Vector of count (genotype or reads) for the reference allele in the second sample</dd>
<dt>totcount1</dt>
<dd>Vector of total count or read coverages in the first sample</dd>
<dt>totcount2</dt>
<dd>Vector of total count or read coverages in the second sample</dd></dl>

Arguments

compute_snpQ2onepair — compute_snpQ2onepair

<dl>

<dt>refcount1</dt>
<dd>Vector of count (genotype or reads) for the reference allele in the first sample</dd>


<dt>refcount2</dt>
<dd>Vector of count (genotype or reads) for the reference allele in the second sample</dd>


<dt>totcount1</dt>
<dd>Vector of total count or read coverages in the first sample</dd>


<dt>totcount2</dt>
<dd>Vector of total count or read coverages in the second sample</dd>

</dl>

compute_snpQ2onepair: compute_snpQ2onepair

Description

Usage

Value

Arguments

Details

Examples