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

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

S4 class to represent a Count data set.

Description

S4 class to represent a Count data set.

Slots

npops

The number of populations

nsnp

The number of SNPs

refallele.count

A matrix (nsnp rows and npops columns) with the allele counts for the reference allele

total.count

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)

snp.info

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)

popnames

A vector of length npops with the corresponding population names

See Also

To generate countdata object, see genobaypass2countdata and genotreemix2countdata

poolfstat documentation built on April 4, 2025, 1:49 a.m.