Principal component (PC) projector for ancestry

PC-projector is an R script that calculates reference-projected principal components (PCs) based on genetic data. Projection of PCs is is useful when you want the PC to be independent of the target sample. The R-script does this using PLINK v1.9. First using the reference genetic data provided, a list of SNPs that are LD independent and suitable for calculating ancestry is made. Then PCs based on the reference sample are projected into the target sample. The PCs are then scaled to the reference sample (i.e. the reference mean is subtracted from each score, and divided by the reference standard deviation).

Getting started

Prerequisites

R and the required packages:

install.packages(c('data.table','optparse','foreach','doMC'))

PLINK 1.9 software
Reference genetic data
- Binary PLINK format (.bed/.bim/.fam)
Target sample genetic data
- Binary PLINK format (.bed/.bim/.fam)
- RSIDs should match the reference data
- The data should not contain any duplicate RSIDs

Parameters

Flag	Description	Default
--target_plink_chr	Path to per chromosome target PLINK files (.bed/.bim/.fam)	NA
--ref_plink_chr	Path to per chromosome reference PLINK files (.bed/.bim/.fam)	NA
--plink	Path PLINK software binary	plink
--output	Name of output files. Set it to be in an empty directory.	./PC_projector_output/Output
--batch_size	Number of individuals in each batch	5000
--n_pcs	Number of PCs to extract	20

Output files

In the specified output directory, the following files will be produced:

Name	Description
.eigenvec	File containing projected PC scores for the target sample
.log	Log file.

Examples

These examples use FUSION 1KG reference data (download).

When using default settings:

Rscript ./PC_projector.R \
--target_plink_chr ./FUSION/LDREF/1000G.EUR. \
--ref_plink_chr ./FUSION/LDREF/1000G.EUR. \
--plink ./Software/plink1.9 \
--output ./PC_projector_demo/PC_projections \
--n_pcs 100

Help

This script was written by Dr Oliver Pain.

If you have any questions or comments please contact me at oliver.pain@kcl.ac.uk

opain/PC-projector