remove_linked_snps: Method to select snps so that they are not in LD.

In richardslab/MRutils: Utility functions for preparing data for Two-Sample MR

Description

Method to select snps so that they are not in LD.

Usage

remove_linked_snps(
  input_snps,
  pop,
  token = Sys.getenv("LDLINK_TOKEN"),
  prune_r2_threshold = 0.05
)

Arguments

input_snps	a dataframe
pop	the population codes (or vector thereof) in which the LD is calculated e.g. c("CEU"), c("CEU","YRI")
token	is an access token to the nci API. if you don't have a token go here: https://ldlink.nci.nih.gov/?tab=apiaccess
prune_r2_threshold	a threshold (in LD r^2) for two SNPs to be considered "close"

Value

a list with the pruned dataframe, the list of removed SNPs, and three plots (if ggplot2 is available)

richardslab/MRutils documentation built on Dec. 22, 2021, 4 p.m.