Working with data

Overview

Originally presented: Day 2, June 2, 2026
Lead: Lead: Elizabeth Prom-Wormley
Topics: assumptions, QC, imputation, PLINK and R basics, phenotype distributions, and transformations

Additional Reference Reading

Anderson et al 2010 Nat Protoc Data quality control in genetic case-control association studies https://pmc.ncbi.nlm.nih.gov/articles/PMC3025522/
Winkler et al 2014 Nat Protoc; Quality control and conduct of genome-wide association meta-analyses https://pmc.ncbi.nlm.nih.gov/articles/PMC4083217/
Uffemann et al 2021 Nature Reviews Methods Primers; Genome-wide association studies (great overall summary with great tables, boxes and a list of references to specific topics) https://research.vu.nl/ws/portalfiles/portal/155815846/Genome_wide_association_studies.pdf

Lectures

Working with SNP level data (40 minutes)

This lecture series can be viewed as a YouTube playlist.

This series of lectures can be viewed as a YouTube playlist.

Some students really enjoy using Swirl to learn R https://swirlstats.com/students.html

Students are also welcome to walk through a 4-part introduction with videos and the accompanying scripts/data. This series of videos is appropriate for learners who haven’t had prior exposure to R (or limited exposure) and who want to prepare to successfully participate in hands-on-activities throughout the workshop. By the end of the videos, learners will be able to produce basic summary statistics with phenotypic data that would typically be conducted prior to GWAS.