Genetic matching can be achieved via PCA [10, 11, 17], the SGA [12], or based on measures of identity by state [18]. Various software programs are available for estimating ancestry; for example, Eigenstrat [11], PLINK [46], and SpectralGEM [12]. Given pairwise distances or similarities, strata can be formed using the fullmatch algorithm, implemented in R (cran.r-project.org) via the optmatch library [31]. Finally, provided the pseudo-controls are delineated, and the matched strata defined, analysis can be performed using any standard software for conditional logistic analysis. For example, the clogit function, part of the survival library is available in R. We provide a suite of R programs to implement all of the algorithms necessary to perform the full set of analyses described herein from our website (see mCLR source code).
