countdata-class

countdata

S4 class to represent a Count data set.

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

countdata-class function

<dl>
<dt><code>npops</code></dt>
<dd>The number of populations</dd></dl>
<dt><code>nsnp</code></dt>
<dd>The number of SNPs</dd>
<dt><code>refallele.count</code></dt>
<dd>A matrix (nsnp rows and npops columns) with the allele counts for the reference allele</dd>
<dt><code>total.count</code></dt>
<dd>A matrix (nsnp rows and npops columns) with the total number of counts (i.e., twice the number of genotyped individual for diploid species and autosomal markers)</dd>
<dt><code>snp.info</code></dt>
<dd>A data frame (nsnp rows and 4 columns) detailing for each SNP, the chromosome (or scaffold), the position, Reference allele name and Alternate allele name (if available)</dd>
<dt><code>popnames</code></dt>
<dd>A vector of length npops with the corresponding population names</dd>

Slots

S4 class to represent a Count data set. — countdata-class

<dl>
<dt><code>npops</code></dt>
<dd>The number of populations</dd>


<dt><code>nsnp</code></dt>
<dd>The number of SNPs</dd>


<dt><code>refallele.count</code></dt>
<dd>A matrix (nsnp rows and npops columns) with the allele counts for the reference allele</dd>


<dt><code>total.count</code></dt>
<dd>A matrix (nsnp rows and npops columns) with the total number of counts (i.e., twice the number of genotyped individual for diploid species and autosomal markers)</dd>


<dt><code>snp.info</code></dt>
<dd>A data frame (nsnp rows and 4 columns) detailing for each SNP, the chromosome (or scaffold), the position, Reference allele name and Alternate allele name (if available)</dd>


<dt><code>popnames</code></dt>
<dd>A vector of length npops with the corresponding population names</dd>


</dl>

countdata-class: S4 class to represent a Count data set.

Description

Arguments

Slots

See Also