Description Usage Arguments Value References
We follow the Bulik-Sullivan et al. (2015) approach but use a robust LS estimation. The input r2 is the averaged reference LD scores (scaled by the total number of SNPs used to compute the LD scores). The weight W is typically based on the LD scores computed using HapMap3 common SNPs to correct over-counting.
1 |
Zs |
Mx2 matrix of summary Z-statistics for M variants from two GWAS |
r2 |
average reference LD scores for M variants |
N1 |
sample size for the 1st GWAS |
N2 |
sample size for the 2nd GWAS |
Nc |
overlapped sample size between the two GWAS |
W |
variant weight |
genetic covariance
genetic correlation
estimated intercept, quantifying the marginal trait correlation
SNP heritabilities
Bulik-Sullivan,B.K. et al. (2015) An atlas of genetic correlations across human diseases and traits. Nat. Genet. 47, 1236–1241.
Guo,B. and Wu,B. (2018) Principal component based adaptive association test of multiple traits using GWAS summary statistics. bioRxiv 269597; doi: 10.1101/269597
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