SNPannotator (version 1.4.3)

findPairwiseLD: Computes and returns LD values between the given variants.

Description

This function returns a data frame of LD values between the given variants in a selected population.

Usage

findPairwiseLD(
  rsList,
  file = NULL,
  pairwise = FALSE,
  build = 38,
  db = "1000GENOMES:phase_3:EUR",
  r2 = 0.1
)

Value

A data table with variant information.

Arguments

rsList

A vector of rs numbers.

file

Path to the Excel file for saving search results.

pairwise

If TRUE, compute pairwise LD between all elements of a list. If FALSE, computes the LD between first and other elements of the list. default: FALSE

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"

r2

Only return pairs of variants whose r-squared value is equal to or greater than the value provided. default: 0.1.