agenda.md

Draft Schedule (idea: Starting in September 2021)

Session 0: First get-together and planning session

• Date: Sep 10, 2021

Session 1: What is Principal Component analysis?

• Date: Sep 17, 2021
• Presenters: Yilei, Divyaratan
• Reading: PCA chapter of History and geography of human genes (mattermost)
• Reading: https://liorpachter.wordpress.com/2014/05/26/what-is-principal-component-analysis/
• Reading: Novembre et al., “Genes Mirror Geography within Europe.” [@Novembre2008]

Session 2: (Practical): How to use PCA?

• Date: Sep 24, 2021
• Presenters: Stephan, Thiseas
• Tools: smartpca,
• Data: HGDP, thinned down (?)
• Topics: PCA, F2, MDS, connections between them

Session 3: Missing data and projection

• Date: Oct 8, 2021
• Presenters: Luca, Thiseas
• Reading: Meisner, Jonas, Siyang Liu, Mingxi Huang, and Anders Albrechtsen. 2021. “Large-Scale Inference of Population Structure in Presence of Missingness Using PCA.” Bioinformatics , January. https://doi.org/10.1093/bioinformatics/btab027.
• Reading: Agrawal, Aman, Alec M. Chiu, Minh Le, Eran Halperin, and Sriram Sankararaman. 2020. “Scalable Probabilistic PCA for Large-Scale Genetic Variation Data.” PLoS Genetics 16 (5): e1008773.

Session 4 (Practical): How to deal with missing data

• Date: Oct 15, 2021
• Presenters: Clemens, Ben V.
• Tools: softImpute
• Tool: least square projection
• Approaches
  • mean imputation
  • projection
  • EM-imputation
  • MDS-projection?

Session 5 (Practical): More on projection and PCA

• Date: Oct 22, 2021
• Goal: Try out various missing data techniques

Session 6: Structure / Admixture

• Date: Nov 5, 2021
• Presenters: Leonardo A., Ke
• Reading:
  • Pritchard et al. 2000
  • Alexander et al. 2009 (Admixture)
  • maybe some review (for example Falush "Badmixture")

Session 7 (Practical): How to run Admixture?

• Date: Nov 12, 2021
• Presenters: Sandra, Laura, Joscha
• Tool: ADMIXTURE
• Tasks: Run admixture
  • Run admixture in supervised mode
  • Comparison with PCA
  • PCA on Admixture components (?)
  • Dystruct?

Session 8: Foundational principles behind PCA/Admixture

• Date: Nov 26, 2021
• Presenters: Stephan, Federica, Alba
• Reading: Engelhardt and Stephens, “Analysis of Population Structure.”
• Reading: McVean 2009

Session 9 (Practical): Simulations / predictions

• Date: Dec 10, 2021
• Presenters: Leonardo I., Arev
• Tool: msprime
• Tasks
  • Simulation with sample sizes / coalescence rates
  • Task: Predicted PCA vs Simulations

Session 10: F-Statistics and PCA/MDS

• Date: Dec 17, 2021
• Presenters: Ben Peter
• Reading: https://www.biorxiv.org/content/10.1101/2021.07.13.452141v2

Further topics:

• non-linear projections
  • tSNE
  • UMAP
  • Diffusion maps
• other linear projections
  • Trees
  • Admixture Graphs
  • Treelets
• Comparison of tools
  • Detailed discussion of MDS vs PCA
  • F-statistics and PCA
  • qpADM and PCA
• Selection and SNP outliers
• PCA based on other matrices such as Fine-Structure
• Interpretation of PCA-plots