8.1 Setup

The premise for this exercise is that you’re part of a company developing a cancer drug called .

Today, we’ll perform a GWAS on resistance to two drugs (GS451 and CB1908) in 1000 Genomes lymphblastoid cell lines. The phenotype we’re interested in is \(\mathbf{IC_{50}}\), defined as the concentration of the drug at which the cells experience 50% viability.

8.1.1 R packages

In addition to tidyverse, we’ll use vcfR to read in genotype data and qqman to create Manhattan and QQ plots.

library(tidyverse)
library(vcfR)
library(qqman)

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