choose_best_proxies: method to remove ambiguous (palindromic and AF too close to...
In richardslab/MRutils: Utility functions for preparing data for Two-Sample MR

method to remove ambiguous (palindromic and AF too close to 0.5) SNPs and select for the smallest p-value within each "query_rsid":

choose_best_proxies(
  proxies_and_more,
  near_half_threshold = 0.08,
  validate = TRUE
)

`proxies_and_more`	the dataframe containing results from get_proxies merged with an outcome GWAS. The Alleles column is assumed to have been already "fixed" according to the "Correlated_Alleles" column (using fix_alleles).
`near_half_threshold`	The distance from AEF=0.5 that is to be considered "unimbiguous" when a palindromic SNP has it.
`validate`	a boolean indicating whether to validate the resulting gwas (TRUE by default) use FALSE for debugging.

The original dataframe, with palindromic SNPs removed and within each query_rsid only the one with the smallest P value retained. In the case of a tie, the one with the smallest distance to the query SNP (located in POS.exp) will be chosen. In the extremely rare case of a further tie, it will be broken randomly.

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