finemap.signals: Finemap multiple signals in a single dataset

In coloc: Colocalisation Tests of Two Genetic Traits

Finemap multiple signals in a single dataset

Description

This is an analogue to finemap.abf, adapted to find multiple signals where they exist, via conditioning or masking - ie a stepwise procedure

Usage

finemap.signals(
  D,
  LD = D$LD,
  method = c("single", "mask", "cond"),
  r2thr = 0.01,
  sigsnps = NULL,
  pthr = 1e-06,
  maxhits = 3,
  return.pp = FALSE
)

Arguments

D	list of summary stats for a single disease, see check_dataset
LD	matrix of signed r values (not rsq!) giving correlation between SNPs
method	if method="cond", then use conditioning to coloc multiple signals. The default is mask - this is less powerful, but safer because it does not assume that the LD matrix is properly allelically aligned to estimated effect
r2thr	if mask==TRUE, all snps will be masked with r2 > r2thr with any sigsnps. Otherwise ignored
sigsnps	SNPs already deemed significant, to condition on or mask, expressed as a numeric vector, whose names are the snp names
pthr	when p > pthr, stop successive searching
maxhits	maximum depth of conditioning. procedure will stop if p > pthr OR abs(z)<zthr OR maxhits hits have been found.
return.pp	if FALSE (default), just return the hits. Otherwise return vectors of PP
mask	use masking if TRUE, otherwise conditioning. defaults to TRUE

Value

list of successively significant fine mapped SNPs, named by the SNPs

Author(s)

Chris Wallace

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