GWAS.catalog.SNP.proxy: Fetches associations in the GWAS Catalog involving the gived...

In alesssia/timesaveR: Widely used function to save time on everyday work

Fetches associations in the GWAS Catalog involving the gived all proxy SNP

Description

Uses LDproxy Programmatic Access via API (https://ldlink.nci.nih.gov/?tab=ldproxy), to extract the proxy SNPs, and then uses GWAS Catalog Access via API (https://www.ebi.ac.uk/gwas/rest/docs/api) to fetch the GWAS associations. According to the LDLink CoC, this script should be run sequentially. If no associations is found, NULL is returned.

Usage

GWAS.catalog.SNP.proxy(
  rs,
  r2 = c("r2", "d"),
  pop = "GBR",
  LDlinktoken,
  min.r2 = 0.01,
  max.distance = 5e+05
)

Arguments

rs	reference SNP IDs for the variant
r2	whether use r2 or D' (use "r2" and "d", respectively)
pop	population (multiple populations should be formatted as pop1%2pop2%2pop3)
LDlinktoken	personal token (request via https://ldlink.nci.nih.gov/?tab=apiaccess)
min.r2	minum LD (r2) to return
max.distance	maximun distance (in bp) to return

Value

a data frame listing the associations recorded in the GWAS catalog

Author(s)

Alessia Visconti

See Also

LDproxy

GWAS.catalog.SNP

Examples

GWAS.catalog.SNP.proxy("rs7681615", "r2", "GBR", "n0tw0rk1ng", 0.8, 500000)
GWAS.catalog.SNP.proxy("rs4693052", "r2", "GBR", "n0tw0rk1ng", 0.8, 500000)

alesssia/timesaveR documentation built on Jan. 26, 2024, 5:21 p.m.