regional.ABF: regional.ABF

In cnfoley/hyprcoloc: Hypothesis Prioritisation in multi-trait Colocalization (HyPrColoc)

Description

regional.ABF

Usage

regional.ABF(
  Z,
  W,
  snps.clc,
  rho,
  trait.cor,
  sample.overlap,
  epsilon,
  reg.thresh,
  prior.1,
  prior.2,
  prior.3,
  prior.4,
  flag,
  test.2,
  reg.steps,
  cor.adj.priors,
  uniform.priors,
  branch.jump,
  Zsq,
  Wsq,
  ind.traits
)

Arguments

Z	matrix of Z-scores
W	ratio matrix of prior standard deviation and observed standard errors
snps.clc	SNPs colocalisation
rho	LD matrix
trait.cor	correlation matrix between traits
sample.overlap	matrix of sample overlap between traits
epsilon	tolerance parameter
reg.thresh	regional probability threshold
prior.1	prior probability of a SNP being associated with one trait
prior.2	1 - prior probability of a SNP being associated with an additional trait given that the SNP is associated with at least 1 other trait
prior.3	prior probability that a trait contains a second causal variant given it contains one already
prior.4	1 - prior probability that trait two co-localises with trait one given traits one and two already share a causal variant and trait one contains a second causal variant
flag	flag variable
test.2	test for 2CV
reg.steps	regional step paramter
cor.adj.priors	correlation adjusted priors
uniform.priors	uniform priors
branch.jump	branch jump
Zsq	matrix of Z-scores squared
Wsq	matrix of W squared
ind.traits	are the traits independent or to be treated as independent

cnfoley/hyprcoloc documentation built on Feb. 15, 2021, 7:55 p.m.