LD matrices

Components of GWAS summary data

• genome wide
• sample overlap
• distribution of genetic effects
  • polygenic
  • following an evolutionary model
• sparseness
• genetic effects wrt LD patterns
• winner’s curse - top hits have winner’s curse
• large sample sizes
• population structure

library(simulateGP)

pop <- "EUR"
bfile <- paste0("/Users/gh13047/repo/mr-base-api/app/ld_files/", pop)

varref <- variant_reference(bfile)
regions <- get_regions(pop)

t1 <- Sys.time()
generate_ld_matrices(regions[1:2,], varref, bfile)
Sys.time()-t1

t1 <- Sys.time()
generate_ld_matrices2(regions[1:2,], varref, bfile)
Sys.time()-t1