per.snp.priors — per.snp.priors • cophescan

Estimate per snp priors

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 \(pc = p12/p1+p12\)

priors at the query variant

Ichcha Manipur