Calculate sequence diversity

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.

Usage

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.