WinCalcD: Calculate Patterson's D-statistic in sliding windows

In evobiR: Comparative and Population Genetic Analyses

Description

This functions calculate Patterson's D-statistic in windows.

Usage

WinCalcD(alignment = "alignment.fasta", win.size = 100, step.size=50,
boot = F, replicate = 1000)

Arguments

alignment	This is an alignment in fasta format
win.size	This is the size of the window used
step.size	This is the size of steps in the sliding window
boot	This indicates whether or not bootstrapping should be performed to estimate variance
replicate	Number of replicates to be used in estimating variance

Details

This function is just an extension of CalcD and calculates D statistic for windows.

Value

Returns a table with the number of each type of site, Z scores and p-values for each window in the genome

Author(s)

Heath Blackmon

References

http://coleoguy.github.io/

Durand, Eric Y., et al. Testing for ancient admixture between closely related populations. Molecular biology and evolution 28.8 (2011): 2239-2252.

Eaton, D. A. R., and R. H. Ree. 2013. Inferring phylogeny and introgression using RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae). Syst. Biol. 62:689-706

Examples

WinCalcD(alignment = system.file("1.fasta", package = "evobiR"), 
         win.size=100, step.size=50, boot = TRUE, replicate=10)
  

evobiR documentation built on May 2, 2019, 5:40 a.m.