Supplementary:

Gene Set Association Analysis using the Coefficient of Intrinsic Dependence

• R Programs
  assoc_test.r
  exampleData.csv
  
  
  • This R program provides one example of computing CID and
    permutation p-value for the genes in biosynthesis of unsaturated
    fatty acids pathway (predictor gene set) and the genes in graft
    versus host disease pathway (target gene set) in 25T.
    
    
  • Please download and save two files in the same directory.
    
    
  • To run the R code, copy and paste all commands in "assoc_test.r"
    on R console. R is a freely available language and environment for
    statistical computing and graphics. It can be downloaded from
    http://www.r-project.org/
    
    
  • The outputs will show on the R console after the program is
    sucessfully excuted. Please note the permutation p-value would
    be slightly altered due to its nature of randomness.
    
    
• Suppl. Tables and Figures.