R/arisim_marginalisation.R

In danjlawson/badMIXTURE: Validating Structure With Chromosome Painting

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## DATA
#' @title Ari-like Simulated genetic data for the Marginalisation Scenario
#'
#' @description
#' Simulated data set to represent the genetics of the Ari people, as reported in van Dorp et al PLoS Genetics 2015 11(8): e1005397, and followed up in Falush, van Dorp & Lawson \url{http://biorxiv.org/content/early/2016/07/28/066431}.
#'
#' This dataset was simulated to understand the Ari people, who are culturally split into "Blacksmiths" and "Cultivators". There was much discussion whether the Blacksmiths were a better representative of an ancient African population, or whether they were simply marginalised and hence had experienced genetic drift that made them look different to other populations. Package \code{\link{badMIXTURE}} allows you to test exactly this.
#' 
#' This simulation follows the so-called "Marginalisation" scenario, in which the truth is that the "Ari Blacksmiths" (Population 13) are drifted, whilst the "Ari Cultivators" (population 5) are the best representative of the ancestral population. The mixture solution (\code{arisim_marginalisation$mix} produced with ADMIXTURE, Alexander, Novembre & Lange 2009, Genome Research 19:1655-1664) gets this wrong but the residual plots (\code{arisim_marginalisation$data} produced with ChromoPainter, Lawson, Hellenthal, Myers & Falush 2012, PLoS Genetics, e1002453)  highlight this.
#'
#' See \code{\link{compareMixtureToData}}) and the examples within for how to understand this data.
#' 
#' @format arisim_marginalisation contains the following items:
#' \itemize{
#'   \item mixture : the ADMIXTURE (mixture) estimate for these data
#'   \item data : The ChromoPainter results for these data
#'   \item ids : The mapping of individuals into groups 
#' }
#'#' @source \url{http://biorxiv.org/content/early/2016/07/28/066431}
#' @references \url{http://biorxiv.org/content/early/2016/07/28/066431}
"arisim_marginalisation"
#> [1] "arisim_marginalisation"