seqDiversity: Calculate sequence diversity

In maize-genetics/rTASSEL: R Front-End for TASSEL

Calculate sequence diversity

Description

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.

maize-genetics/rTASSEL documentation built on Nov. 13, 2023, 7:18 a.m.