Due date

Monday, April 13, 5pm

Simulated data

Download the simulated dataset HW4.Rda and load it into your R environment.

rm(list = ls())
load("HW4.Rda")
ls()

[1] "chr"        "markerName" "pos"        "W"          "y"         

1. chr: chromosomes
2. markerName: marker names
3. pos: marker position
4. W: marker matrix
5. y: quantitative phenotypes

Question 1

Read Visscher (2008) and summmarize the paper in 200 - 300 words.

Question 2

Perform single-marker mixed linear model GWAS using the rrBLUP package. Create a Manhattan plot and find out which markers are significant under the Bonferroni correction. Use the statistical significance threshold \(\alpha = 0.05\)