Human differentiation analysis

Details on the data analysis for two parallel publications:

• "New kinship and FST estimates reveal higher levels of differentiation in the global human population" by Ochoa and Storey.
  • human-origins-00-preprocessing.pdf: Pre-processing the raw Human Origins data to obtain the files under data/
  • human-origins-01-analysis.pdf: Our analysis of the Human Origins data available under data/.
  • hispanics-00-preprocessing.pdf: Pre-processing the raw 1000 Genomes data to obtain the files under data/
  • hispanics-01-analysis.pdf: Our analysis of the Hispanic individuals in 1000 Genomes data available under data/.
• "FST and kinship for arbitrary population structures II: Method of moments estimators" by Ochoa and Storey.
  • simulations-analysis.pdf: Our analysis of simulated genotype data (randomly generated inside the vignette using the bnpsd package). Considers independent subpopulations (the classical FST setting) and differentially-admixed individuals (a complex population structure only our approach handles correctly).

BED and BIM files on Large File Storage

This repository contains very large files (BED and BIM extensions) stored on GitHub's "Large File Storage", which means that regular git commands like git clone will not download these large files unless the git-lfs extension is installed. After cloning, if the desired files are still missing (small files with the same paths are merely links), you may need to run git lfs pull to retrieve these large files.

See https://git-lfs.github.com/ for more information.

If you have any problems downlading this data, a copy of the entire data/ subdirectory is also available here: http://viiia.org/human-differentiation-manuscript-data.zip