retrieveLD_LDproxy: Retrieve SNP pairwise LD from LDlink database

In dingruofan/xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Retrieve SNP pairwise LD from LDlink database

Description

Retrieve SNP pairwise LD from LDlink database

Usage

retrieveLD_LDproxy(
  targetSnp = "",
  population = "EUR",
  windowSize = 50000,
  method = "download",
  genomeVersion = "grch38",
  max_count = 3,
  token = "9246d2db7917"
)

Arguments

targetSnp	target SNP, support dbSNP IP.
population	Supported population is consistent with the LDlink, which can be listed using function LDlinkR::list_pop()
windowSize	Window around the highlighted snp for querying linkage disequilibrium information. Default:500000
method	The same as fetchContent function, can be chosen from "download", "curl", "GetWithHeader".
genomeVersion	"grch38"(default) or "grch37".
max_count	To prevent download failure due to network fluctuations, max number of connection attempts.
token	Ldlink token, default: "9246d2db7917"

Value

A data.table object.

Examples

# snpLD <- retrieveLD_LDproxy("rs3", windowSize=5000)

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.