PCAmatchR: Match Cases to Controls Based on Genotype Principal Components
PCAmatchR is an open source, R-based software package that enables users to perform optimal case-control matching for more accurate genome-wide association study (GWAS) analyses. By performing analyses of user-supplied principal components, PCAmatchR aids in selecting controls that are well matched by ancestry to cases, thus avoiding biased association results caused by ancestry-based genetic differences between cases and controls.
PCAmatchR takes user-supplied PCA outputs and selects matching controls for cases by utilizing a weighted Mahalanobis distance metric, which weights each principal component by the percent of genetic variation explained.
Brown DW, Myers TA, Machiela MJ. PCAmatchR: A flexible R package for optimal case-control matching using weighted principal components. Bioinformatics 2021 May 23.