flag_gc_conflicts: Flag conflicts with the GWAS catalog

In MRCIEU/mrQC: CheckSumStats

Flag conflicts with the GWAS catalog

Description

Flag conflicts with the GWAS catalog through comparison of reported effect alleles and reported effect allele frequency.

Usage

flag_gc_conflicts(
  dat = NULL,
  beta = "lnor",
  se = "lnor_se",
  efo = NULL,
  trait = NULL,
  efo_id = NULL,
  gwas_catalog_ancestral_group = c("European", "East Asian"),
  exclude_palindromic_snps = TRUE
)

Arguments

dat	the test dataset of interest
beta	name of the column containing the SNP effect size
se	name of the column containing the standard error for the SNP effect size.
efo	trait of interest in the experimental factor ontology
trait	the trait of interest
efo_id	ID for trait of interest in the experimental factor ontology
gwas_catalog_ancestral_group	restrict the comparison to these ancestral groups in the GWAS catalog. Default is set to (c("European","East Asian")
exclude_palindromic_snps	should the function exclude palindromic SNPs? default set to TRUE. If set to FALSE, then conflicts with the GWAS catalog could reflect comparison of different reference strands.

Value

list

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