LDlist: Find variants in high LD with the lead SNP.

In SNPannotator: Investigating the Functional Characteristics of Selected SNPs and Their Vicinity Genomic Region

Find variants in high LD with the lead SNP.

Description

This function returns a list of variables that are in high LD with the lead variant.

Usage

LDlist(rslist, server, db, window_size, r2)

Arguments

rslist	A vector of rs numbers.
server	Name of the server. "https://rest.ensembl.org" can be used for GRCh38 and "https://grch37.rest.ensembl.org" for GRCh37.
db	The population database for calculating LD scores. This can be found using listDatabases function.
window_size	Number of base pairs around the variant for checking LD scores (max = 500kb)
r2	The LD threshold for selecting variants around the target SNP.

Value

a data table with variant information.

SNPannotator documentation built on Jan. 12, 2023, 5:15 p.m.