align.ABF.2: align.ABF.2

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

Description

align.ABF.2

Usage

align.ABF.2(
  Z,
  W,
  snps.clc,
  trait.cor,
  sample.overlap,
  ld.matrix,
  epsilon,
  reg.res,
  align.thresh,
  prior.1,
  prior.2,
  prior.3,
  prior.4,
  cor.adj.priors,
  uniform.priors
)

Arguments

Z	matrix of Z-scores
W	ratio matrix of prior standard deviation and observed standard errors
snps.clc	SNPs colocalisation
trait.cor	correlation matrix between traits
sample.overlap	matrix of sample overlap between traits
ld.matrix	LD matrix
epsilon	tolerance parameter
reg.res	regional result
align.thresh	alignment 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
cor.adj.priors	correlation adjusted priors
uniform.priors	uniform priors

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