ldlinkr_ldproxy_batch: Extract LD proxies from 1KGphase3

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Extract LD proxies from 1KGphase3

Description

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

Usage

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.

Details

merged_query_dat <- echodata::get_Nalls2019_merged() lead.snps <- setNames(subset(merged_query_dat, leadSNP)$Locus, subset(merged_query_dat, leadSNP)$SNP) proxies <- ldlinkr_ldproxy_batch(snp = lead.snps)

Source

website

See Also

Other LD: check_population_1kg(), compute_LD(), filter_LD(), get_LD(), get_LD_1KG(), get_LD_1KG_download_vcf(), get_LD_UKB(), get_LD_matrix(), get_LD_vcf(), get_locus_vcf_folder(), plot_LD(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF()

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.