Input Data
POP Files
The POP (PRS on Phenotype) file specification simply requires two columns of whitespace or comma-separated data where the first column contains PRS values and the second the corresponding Phenotype values. Note that the header is optional for our Python scripts but required by R:
| PRS | Phenotype |
|---|---|
| -2.2 | -1.5 |
| -1.3 | -0.4 |
| -0.3 | -0.1 |
| -0.6 | 0.2 |
| 1.6 | 0.9 |
| 2.1 | 1.3 |
| 2.5 | 2.1 |
If you have PRS and Phenotype data with sample IDs in the first column then you can create a POP file using our Python script as shown with example data:
Creating a POP File
The following command will create POP file named my_file.pop.
./POPout.py --makePOPfile data/TEST.prs data/TEST.pheno -o my_file