evobiR (version 1.1)

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

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

Value

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

Details

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

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)