coloc.susie_bf: run coloc using susie to detect separate signals

In coloc: Colocalisation Tests of Two Genetic Traits

run coloc using susie to detect separate signals

Description

coloc for susie output + a separate BF matrix

Usage

coloc.susie_bf(
  dataset1,
  bf2,
  p1 = 1e-04,
  p2 = 1e-04,
  p12 = 5e-06,
  susie.args = list(),
  ...
)

Arguments

dataset1	a list with specifically named elements defining the dataset to be analysed. See check_dataset for details.
bf2	named vector of log BF, names are snp ids and will be matched to column names of susie object's alpha
p1	prior probability a SNP is associated with trait 1, default 1e-4
p2	prior probability a SNP is associated with trait 2, default 1e-4
p12	prior probability a SNP is associated with both traits, default 1e-5
susie.args	named list of arguments to be passed to susieR::susie_rss()
...	other arguments passed to coloc.bf_bf, in particular prior values for causal association with one trait (p1, p2) or both (p12)

Value

coloc.signals style result

Author(s)

Chris Wallace

coloc documentation built on Oct. 3, 2023, 5:07 p.m.