Computer codes for Francois and Jay Nat. Commun. (2020)

This repository contains R codes for simulation and data analyses from (Francois and Jay, Nat. Commun. 2020). Figures refer to the main text of the manuscript.

Codes for Figure 1

These codes are in the folders Simulation_divergence_models and Simulation_single_population_models

Codes for Figure 1 and for Figure 2

These codes are in the folder Simulation_admixture_models. These analyses require having ADMIXTOOLS installed on the computer system (Linux is preferable for ADMIXTOOLS analyses). We provided a notebook that explains how any analysis in the study could be reproduced with the packages ``tfa(this paper),LEA` (bioconductor), and `admixr` (CRAN).

Codes for Figure 3 and related supplementary figures

These codes are in the folder Data_analysis_704_samples, reproducing FA and PC projections for all ancient samples in the study. The data must be loaded before analysis. Open the R script and copy the url for downloading them from an external repository (Github does not accept large data sets).

Codes for Figure 4 and related supplementary figures. Figures S10 - S12

These codes are in the folder Two_way_admixture_analyses. Two-way admixture analyses of European samples. These analyses require to have ADMIXTOOLS installed, and to place some data files in the "snp" folder (see README file).

Codes for Figure 5 and 6 and related supplementary figures

These codes are in the folder Example_European_samples and reproduce the analyses in Figure 5 and Figure 6

Important Note: Some scripts have been improved by the latest release of the R package 'tfa', and their use may be obsolete. Prefer using the latest version of the package.