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)