ExampleDataset: Allele frequencies from a simulated Evolve and Resequence...

In MartaPelizzola/haploSep: Haplotype Separation with Finite Alphabet Lloyds algorithm

Allele frequencies from a simulated Evolve and Resequence experiment

Description

Simulated allele frequencies with pool sequencing noise. An Evolve and Resequence experiment is simulated for 150 generations and the allele frequency data are available every 10 generations starting at time point 0.

Format

A matrix with nrow(Y)=500 observations on ncol(Y)=16 variables.

Details

This simulated data are generated from a set of founder haplotypes from "Genetic redundancy fuels polygenic adaptation in Drosophila", Barghi et al. (2019). Additionally, haplotype frequencies are simualated to mimic an Evolve and Resequence experiment lasting 150 generations. Then allele frequencies are computed as the product of the haplotype structre and frequency matrix. Pool sequencing noise, as a binomial sampling step, is added to the allele frequencies to obtain this data set.

Examples

data(ExampleDataset)
str(Y) 
matplot(t(Y), type = "l", ylim = c(0,1), ylab = "Allele frequencies", xlab = "Generations", xaxt = "n")
axis(1, at = 1:16, labels=seq(0,150,10))

MartaPelizzola/haploSep documentation built on May 26, 2023, 11:36 a.m.