Retrieve SNP pairwise LD from LDlink database

Retrieve SNP pairwise LD from LDlink database

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)