Generate LD matrices

library(gwasglue)
library(data.table)

For each region generate an LD matrix

pop <- "EUR"
ldref <- paste0("/Users/gh13047/repo/mr-base-api/app/ld_files/", pop)
bim <- data.table::fread(paste0(ldref, ".bim"))
regionfile <- system.file("extdata", "ldetect", paste0(pop, ".bed"), package="gwasglue")
regions <- data.table::fread(regionfile, header=TRUE) %>%
    dplyr::mutate(
        chr=as.numeric(gsub("chr", "", chr)),
        start=as.numeric(start),
        stop=as.numeric(stop)
    ) %>% dplyr::as_tibble()

for(i in 1:nrow(regions))
{
    message(i)
    x <- subset(bim, V1 == regions$chr[i] & V4 >= regions$start[i] & V4 <= regions$stop[i])$V2
    y <- ieugwasr::ld_matrix(x, pop=pop, bfile=ldref, plink_bin=genetics.binaRies::get_plink_binary(), with_alleles=FALSE)
    save(y, file="temp.rdata")
}

bin/emeraLD -i /mnt/storage/private/mrcieu/research/mr-eve/vcf-reference-datasets/1000g/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz –region 6:2458936-3573593 –out ~/mr-eve/temp.ld –no-phase

bin/emeraLD -i /mnt/storage/private/mrcieu/research/mr-eve/vcf-reference-datasets/1000g/1kg_v3_nomult.vcf.gz –region 1:30923-100923 –out ~/mr-eve/temp.ld –no-phase

bin/emeraLD -i /mnt/storage/private/mrcieu/research/mr-eve/vcf-reference-datasets/1000g/temp.vcf.gz –region 6:2458936-3573593 –out ~/mr-eve/temp.ld –no-phase

betas <- hyprcoloc::test.betas ses <- hyprcoloc::test.ses trait.cor <- hyprcoloc::test.corr ld.matrix <- hyprcoloc::test.ld traits <- paste0(“T”, 1:dim(betas)[2]) rsid <- rownames(betas) res <- hyprcoloc(betas, ses, trait.names=traits, snp.id=rsid) res