GRS
The grs module supports genetic risk score workflows on RAP, including weight-file validation, BGEN to PGEN conversion, chromosome-level scoring, score standardisation, and association validation.
Scope
| Function | Role |
|---|---|
grs_check() |
Validate SNP weight files |
grs_bgen2pgen() |
Submit BGEN to PGEN conversion jobs |
grs_score() |
Compute chromosome-level GRS with plink2 |
grs_standardize() |
Standardise score columns |
grs_zscore() |
Alias for score standardisation |
grs_validate() |
Estimate OR, HR, trend, AUC, or C-index summaries |
Workflow Role
Use grs_check() before submitting cloud jobs. Conversion and scoring should run in RAP job environments where plink2 is available. Final score columns can be standardised and passed to grs_validate() or the general assoc_*() functions.
Review Focus
- strict validation of chromosome, allele, and weight columns;
- robust command construction for RAP job submission;
- predictable output file names across chromosomes;
- summary-level validation outputs that are safe to export.