find_hits_in_gwas_catalog: Are hits in the GWAS catalog?

In MRCIEU/mrQC: CheckSumStats

Are hits in the GWAS catalog?

Description

Identify GWAS hits in the test dataset and see if they overlap with GWAS hits in the GWAS catalog.

Usage

find_hits_in_gwas_catalog(
  gwas_hits = NULL,
  trait = NULL,
  efo = NULL,
  efo_id = NULL,
  distance_threshold = 25000
)

Arguments

gwas_hits	the "GWAS hits" in the test dataset (e.g. SNP-trait associations with P<5e-8)
trait	the trait of interest
efo	trait of interest in the experimental factor ontology
efo_id	ID for trait of interest in the experimental factor ontology
distance_threshold	distance threshold for deciding if the GWAS hit in the test dataset is present in the GWAS catalog. For example, a distance_threshold of 25000 means that the GWAS hit in the test dataset must be within 25000 base pairs of a GWAS catalog association, otherwise it is reported as missing from the GWAS catalog.

Value

list

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