abrahamnunes/ldscorejulia.jl

LDScoreJulia

LDSC implementation based on (1) implemented in Julia.

To Do

• ld_score_regression is not complete
• estimate_h2
  • Only has one test case
  • Lots of error checks missing
• Build struct Gencov the same way Hsq is built to reuse abstract type LD_Score_Regression functions

Note. Ignore files that start with Fake or fake.

Estimating SNP-hertiability from summary statistics

To estimate SNP-heritability, we need three sources of data:

1. Summary statistics from a GWAS.
2. List of SNPs.
3. LD scores for each SNP.

LD scores for European and Asian populations can be directly downloaded from the original LDSC website.

LD Score Regression

LD Score regression quantifies contribution of polygenic signals and confounding biases in the inflation of the distribution of test statistic in genome-wide association studies (1); it does this by examinig the relationship between test statistics and linkage disequilibrium

References

1. Schizophrenia Working Group of the Psychiatric Genomics Consortium, Bulik-Sullivan BK, Loh P-R, Finucane HK, Ripke S, Yang J, et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat Genet. 2015 Mar;47(3):291–5.