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:

Column	Description
FID	Family ID (same as IID for FG)
IID	Sample ID
PCn	Value of the nth principal component

Columns in the finngen_R[RELEASE]_eigenvec.varfile:

Column	Description
#CHROM	Chromosome number
ID	Variant name
MAJ	Major allele
NONMAJ	Non-major allele
PCn	Loading of the nth principal component

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?