Extract LD proxies from 1KGphase3

Source: R/ldlinkr_ldproxy_batch.R

Wrapper for LDlinkR::LDproxy_batch. Easy to use but doesn't scale up well to many SNPs (takes way too long).

ldlinkr_ldproxy_batch(
  snp,
  pop = "CEU",
  r2d = "r2",
  min_corr = FALSE,
  save_dir = NULL,
  verbose = TRUE
)

Arguments

snp

a character string or data frame listing rsID's or chromosome coordinates (e.g. "chr7:24966446"), one per line
pop

a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU"
r2d

either "r2" for LD R2 or "d" for LD D', default = "r2"
min_corr

Minimum correlation with snp.
save_dir

Save folder.
verbose

Print messages.

Source

website

Details

data("merged_DT") lead.snps <- setNames(subset(merged_DT, leadSNP)$Locus, subset(merged_DT, leadSNP)$SNP) proxies <- ldlinkr_ldproxy_batch(snp = lead.snps)

See also

Other LD: LD_1KG_download_vcf(), LD_1KG(), LD_custom(), LD_ukbiobank(), compute_LD(), filter_LD(), get_locus_vcf_folder(), load_or_create(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF(), translate_population()