seqDiversity.Rd
This performs basic diversity analyses on genetic data, specifically, average pairwise divergence (\(\pi\)), segregating sites, estimated mutation rate (\(\theta\), or \(4N\mu\)), and Tajima's D can be calculated, as well as sliding windows of diversity.
seqDiversity(
tasObj,
startSite = 0,
endSite = NULL,
slidingWindowAnalysis = FALSE,
stepSize = 100,
windowSize = 500
)
An object of class TasselGenotypePenotype
that
contains a genotype table.
Start site.
End site. Defaults to the maximum index of markers.
Do you want to analyze diversity in a sliding
window? Defaults to FALSE
.
Step size.
Window size.