# Polygenic risk scores (PRS)

This page has been last updated for R11.

### Sandbox directory

Polygenic risk scores (PRS) are available in the following Sandbox directory:

`/finngen/library-red/finngen_R[RELEASE]/prs_1.0`

### Data files

The PRS data files are available for specific studies in the `/data` subdirectory.

The following types of files are available:

* Score files
* Weight files
* Correlation files

Please refer to the readme file in the sandbox directory for full details of the available data.

#### Score files

* `finngen_R[RELEASE]_[STUDY].sscore`: Individual scores for the specific study
* `finngen_R[RELEASE]_[STUDY].no_regions.sscore`: Individual scores with regions removed

Score files are produced using the [plink](https://www.cog-genomics.org/plink/2.0/formats) `-score` option and contain the following tab-separated columns:

| **Column**                 | **Description**             |
| -------------------------- | --------------------------- |
| #FID                       | Family ID                   |
| IID                        | Sample ID                   |
| NMISS\_ALLELE\_C           | Non-missing allele count    |
| NAMED\_ALLELE\_DOSAGE\_SUM | Sum of named allele dosages |
| SCORE1\_AVG                | Score                       |

#### Weight files

* `finngen_R[RELEASE]_[STUDY].weights.txt:` SNP weights produced by PRS-CS

Weight files are produced by PRScs. They contain the following tab-separated columns without column headers:

|            |                 |
| ---------- | --------------- |
| **Column** | **Description** |
| 1          | CHROM           |
| 2          | SNP             |
| 3          | POS             |
| 4          | REF             |
| 5          | ALT             |
| 6          | WEIGHT          |

#### Correlation files

* `finngen_R[RELEASE]_prs_pheno_corr.tsv:` GLM ross correlation between all PRS studies and all other phenotypes, sorted by p-value and filtered for p < 0.0001

Correlation files contain the following tab-separated columns:

| **Column** | **Description**                      |
| ---------- | ------------------------------------ |
| PHENO      | Phenotype                            |
| beta       | Type II error prob. (beta statistic) |
| pval       | p-value                              |
| p\_R2      | p R-squared value                    |
| pval\_F    | P-value of F-statistics              |
| study      | Study name                           |

### Further information

See also the [Using polygenic risk scores](/background-reading/using-prs-data.md) and [how to run PRS](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-prs.md) sections.


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