make_snplist: make a SNP list

In MRCIEU/mrQC: CheckSumStats

make a SNP list

Description

Create a list of rsids corresponding to "top hits" in the GWAS catalog, the 1000 genomes super popualtions and SNPs of specific interest to the user (e.g. genetic instruments/proxies for the exposure of interest).

Usage

make_snplist(
  trait = NULL,
  efo_id = NULL,
  efo = NULL,
  ref1000G_superpops = TRUE,
  snplist_user = NULL
)

Arguments

trait	the name of the trait in the NHGRI-EBI GWAS catalog
efo_id	experimental factor ontology ID for trait of interest
efo	experimental factor ontology for the trait of interest
ref1000G_superpops	include reference SNPs from 1000 genomes super populations. Default=TRUE
snplist_user	character vector of user specified rsids.

Value

character vector

Examples

snplist<-make_snplist(efo_id="EFO_0006859",ref1000G_superpops=FALSE) 

MRCIEU/mrQC documentation built on May 6, 2023, 1:40 p.m.