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
)

## Arguments

tasObj

An object of class TasselGenotypePenotype that contains a genotype table.

startSite

Start site.

endSite

End site. Defaults to the maximum index of markers.

slidingWindowAnalysis

Do you want to analyze diversity in a sliding window? Defaults to FALSE.

stepSize

Step size.

windowSize

Window size.