Univariate LDSC

Imported here to help estimate sample overlap between studies

Usage

ldsc_h2(id, ancestry = "infer", snpinfo = NULL, splitsize = 20000)

Arguments

id

ID to analyse

ancestry

ancestry of traits 1 and 2 (AFR, AMR, EAS, EUR, SAS) or 'infer' (default) in which case it will try to guess based on allele frequencies

snpinfo

Output from ieugwasr::afl2_list("hapmap3"), or NULL for it to be done automatically

splitsize

How many SNPs to extract at one time. Default=20000

Value

model fit

References

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

Gua,B. and Wu,B. (2019) Integrate multiple traits to detect novel trait-gene association using GWAS summary data with an adaptive test approach. Bioinformatics. 2019 Jul 1;35(13):2251-2257. doi: 10.1093/bioinformatics/bty961.

https://github.com/baolinwu/MTAR