per.snp.priors: per.snp.priors

In ichcha-m/cophescan: Adaptation of the Coloc Method for PheWAS

per.snp.priors

Description

Estimate per snp priors

Usage

per.snp.priors(
  nsnps,
  pa = 3.82e-05,
  pc = 0.00182,
  p1 = NULL,
  p2 = NULL,
  p12 = NULL
)

Arguments

nsnps	number of SNPs
pa	prior probability that a non-query variant is causally associated with the query trait (cophescan prior), default 3.82e-5
pc	prior probability that the query variant is causally associated with the query trait (cophescan prior), default 1.82e-3 (cophescan prior)
p1	prior probability a SNP is associated with trait 1, (coloc prior), pc derived by using pc = p12/p1+p12; use p1, p2, p12 only when pa and pc are unavailable (See vignettes)
p2	prior probability a SNP is associated with trait 2, (coloc prior), pa derived by using pa = p2
p12	prior probability a SNP is associated with both traits, (coloc prior), pc derived by using pc = p12/p1+p12

Value

priors at the query variant

Author(s)

Ichcha Manipur

ichcha-m/cophescan documentation built on June 16, 2024, 1:39 a.m.