SNPannotator (version 1.4.3)

findProxy: Finds variants in high LD

Description

This function returns a list of variables that are in high LD with a list of selected variants using data from the Ensembl website.

Usage

findProxy(
  rslist,
  file = NULL,
  build = "38",
  db = "1000GENOMES:phase_3:EUR",
  window_size = 500,
  r2 = 0.8
)

Value

A data table with variant information.

Arguments

rslist

A vector of rs numbers.

file

Path to the Excel file for saving search results.

build

Genome build. Either 37 or 38. default: 38

db

The population database for calculating LD scores. This can be found using Ensembl.Databases() function. default: 1000GENOMES:phase_3:EUR

window_size

Number of base pairs around the variant for checking LD scores (max = 500kb). default: 500

r2

The minimum LD threshold for selecting variants around the target SNP. default: 0.8.