How to create artificial or dummy phenotype data

Question

I have whole genome sequence (human) data (SNP data), but don't have phenotype data ready for any traits yet. Hopefully, I will get real phenotype data soon. To run GWAS (genome-wide-association study) or any other analysis, i want to create artificial/dummy data for any trait, let's say human height. Could anyone please recommend what is best option? Does plink generate any dummy phenotype data? or any other programme?

Answer 1

Using wakefield package it is pretty easy, here is an example from GitHub page. This will create 500 dummy variables for id, race, age, etc. :

library(wakefield)

myDummyPheno <- r_data_frame(
  n = 500,
  id,
  race,
  age,
  sex,
  hour,
  iq,
  height,
  died
)

# result
myDummyPheno

# # A tibble: 500 x 8
#    ID    Race        Age Sex    Hour           IQ Height Died 
#   <chr>  <fct>     <int> <fct>  <S3: times> <dbl>  <dbl> <lgl>
#  1 001   Bi-Racial    27 Male   00:00:00     93.0   71.0 F    
#  2 002   White        28 Female 00:00:00    104     64.0 T    
#  3 003   Black        28 Male   00:00:00    111     67.0 T    
#  4 004   Hispanic     35 Male   00:00:00     90.0   67.0 T    
#  5 005   Hispanic     21 Female 00:00:00     94.0   70.0 T    
#  6 006   Black        35 Male   00:00:00     74.0   73.0 F    
#  7 007   Black        27 Male   00:00:00    102     68.0 T    
#  8 008   White        28 Female 00:00:00     95.0   70.0 F    
#  9 009   White        30 Female 00:00:00     80.0   71.0 F    
# 10 010   White        30 Female 00:00:00    114     66.0 T