This folder contains R script and RData to generate the main Figures from Wang et al. (2020): Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations
Source code of a custom C++ used to calculate LD-based statistics Compile C++ code
make
./ldcorpair --help
Options
--bfile : Binary PLINK format for genotypes.
--snplist : Specify the list of SNPs containing the target SNPs.
--window-kb : Specify the window size to calculate LD correlations. Default is 100 kb.
--out : A prefix for the output file [prefix].ldcor.pairs.
[Note] Missing values are imputed to the major allele.
Overview of output
CHR SNP1 SNP2 POS1_KB POS2_KB A1_1 A1_2 A2_1 A2_2 FREQ_A1_1 FREQ_A1_2 R_LD R_LD_SQ R_LD_SQ_CORR
1 rs28536514 rs58686784 910.409 810.78 C C T G 0.19062 0.304841 0.103561 0.0107248 0.00920504
1 rs28536514 rs114224245 910.409 811.136 C C T G 0.19062 0.0234493 0.00218953 4.79404e-06 -0.00151496
The annotated R script: "Annotated_script_to_calculate_expected_relative_acccuracy.R" was added in Dec 2021 and used in Okbay et al. (2021) to calculate the expected relative accuracy of a Polygenic Score predicting educational attainment in a European ancestries sample relative to an African ancestries sample. The same method was used in Wang et al. (2020).