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
TasselGenotypePenotypethat 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.