# Principal components analysis (PCA) data

This page has been last updated for R11.

### Sandbox directory

Principal components analysis (PCA) data is available in the following Sandbox directory:

`/finngen/library-red/finngen_R[RELEASE]/pca_1.0`

### Data files

The following types of files are available:

* PCA files
* Sample list files

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

#### PCA files

PCA files are in the `/data` subdirectory.

* `finngen_R[RELEASE].eigenval.txt`: List of eigenvalues of PCA. The nth line contains the eigenvalue for the nth principal component.
* `finngen_R[RELEASE].eigenvec.txt`: Principal components of all samples used in the analysis.
* `finngen_R[RELEASE]_eigenvec.var`: Loading of each variant.

Columns in the `finngen_R[RELEASE].eigenvec.txt` file:

<table data-header-hidden><thead><tr><th width="314"></th><th></th></tr></thead><tbody><tr><td><strong>Column</strong></td><td><strong>Description</strong></td></tr><tr><td>FID</td><td>Family ID (same as IID for FG)</td></tr><tr><td>IID</td><td>Sample ID</td></tr><tr><td>PCn</td><td>Value of the nth principal component</td></tr></tbody></table>

Columns in the `finngen_R[RELEASE]_eigenvec.var`file:

<table data-header-hidden><thead><tr><th width="316"></th><th></th></tr></thead><tbody><tr><td><strong>Column</strong></td><td><strong>Description</strong></td></tr><tr><td>#CHROM</td><td>Chromosome number</td></tr><tr><td>ID</td><td>Variant name</td></tr><tr><td>MAJ</td><td>Major allele</td></tr><tr><td>NONMAJ</td><td>Non-major allele</td></tr><tr><td>PCn</td><td>Loading of the nth principal component</td></tr></tbody></table>

#### Sample list files

Sample list files are in the `/data` subdirectory.

These files may have a single column of sample IDs or they may be in the Fam format. A file in the Fam format contains two tab-separated columns that both have the same sample IDs.

* `finngen_R[RELEASE]_unrelated.txt`: Fam file of unrelated samples used for final PCA.
* `finngen_R[RELEASE]_related.txt`: Fam file of samples related to the previous group projected onto their PC space.
* `finngen_R[RELEASE]_rejected.txt`: Fam file of rejected samples.
* `finngen_R[RELEASE]_duplicates.txt`: List of duplicate samples.
* `finngen_R[RELEASE]_total_ethnic_outliers.txt`: List of samples not of Finnish ancestry.
* `finngen_R[RELEASE]_final_samples.txt`: Fam file of all samples included in analysis.

#### Further information

See also: FAQ [Where can I find a list of inrelated individuals in FinnGen?](/faq/about-finngen-data/where-can-i-find-a-list-of-unrelated-individuals-in-finngen.md)


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