Precomputed LD within the BST1 locus (defined in BST1. LD derived British, European-decent subpopulation in the UK Biobank. Only includes a subset of all the SNPs for storage purposes (including the lead GWAS/QTL SNP).

data("BST1_LD_matrix")

Format

data.table

SNP

SNP RSID

CHR

Chromosome

POS

Genomic position (in basepairs)

...

Optional: extra columns

UK Biobank Nalls 2019

matrix

Source

data("BST1") finemap_DT <- BST1 # Only including a small subset of the full # LD matrix for storage purposes. lead_snp <- subset(finemap_DT, leadSNP)$SNP snp_list <- finemap_DT[which(finemap_DT$SNP == lead_snp) - 100:which(finemap_DT$SNP == lead_snp) + 100, ]$SNP BST1_LD_matrix <- readRDS("../Fine_Mapping/Data/GWAS/Nalls23andMe_2019/BST1/plink/UKB_LD.RDS") BST1_LD_matrix <- BST1_LD_matrix[snp_list, snp_list] usethis::use_data(BST1_LD_matrix, overwrite = T)

Details

Data originally comes from UK Biobank. LD was pre-computed and stored by the Alkes Price lab (see here).