Precomputed LD within the BST1 locus
(defined in BST1.
LD derived white British 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")data.table
SNP RSID
Chromosome
Genomic position (in basepairs)
Optional: extra columns
https://www.ukbiobank.ac.uk
https://doi.org/10.1038/s41588-020-00735-5
@examples
data("BST1")
# Only including a small subset of the full
# LD matrix for storage purposes.
lead_snp <- subset(BST1, leadSNP)$SNP
snp_list <- BST1[which(BST1$SNP==lead_snp)-
seq(100,which(BST1$SNP==lead_snp))+100,]$SNP
path <- portal_query(phenotypes = "parkinson",
loci = "BST1",
dataset_types = "LD",
LD_panels = "UKB")
# path <- file.path(
# "../Fine_Mapping/Data/GWAS/Nalls23andMe_2019/BST1/plink/UKB_LD.RDS")
BST1_LD_matrix <- readRDS(path)
BST1_LD_matrix <- BST1_LD_matrix[snp_list, snp_list]
### shortcut
# BST1_LD_matrix <- echolocatoR::BST1_LD_matrix
usethis::use_data(BST1_LD_matrix, overwrite=TRUE)
Data originally comes from UK Biobank. LD was pre-computed and stored by the Alkes Price lab (see here).