1 Introduction

PolyGenic Scores provide a key formulation of genetic findings into disease prediction. There has been a fair amount of concern over the accuracy, confounding and equitability of PGSs. I believe the best way to judge the significance of these worries, and more importantly, ultimately work towards their resolve, is through well-doccumented research.

Quick note on set-up. I am writing this book within a sub-directory of my larger project directory. Hopefully everything will work this way.

1.1 Directory Framework

If you would like to follow along, I would like to make clear how the directories are constructed.

list.files("..")

##  [1] "adjust_ss"          "analyze_score"      "book"              
##  [4] "common"             "do_score"           "images"            
##  [7] "local_scripts"      "med_scripts"        "mod_sets"          
## [10] "old_scripts"        "qc"                 "raw_ss"            
## [13] "verify_toy_example"

I am currently writing in the book directory, one level above will lead to all of the relevant sub-directories. The second and third chapters on summary statistics take place within the directory raw_ss, the fourth chapter on adjusting summary statistics takes place in adjust_ss, . The common, finn_gen, and a few other diretories are indirectly called within scripts outside their own directory. Full paths will be used, so it should be clear where everything is at all times.