BST1_LD_matrix: LD with the lead SNP: BST1 locus

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

LD with the lead SNP: BST1 locus

Description

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).

Usage

data("BST1_LD_matrix")

Format

data.table

SNP

SNP RSID

CHR

Chromosome

POS

Genomic position (in basepairs)

...

Optional: extra columns

Details

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

Source

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)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.