finemap.signals: Finemap multiple signals in a single dataset

Description Usage Arguments Value Author(s)

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

1
2
3
4
5
6
7
8
9
finemap.signals(
  D,
  LD = D$LD,
  method = c("single", "mask", "cond"),
  r2thr = 0.01,
  sigsnps = NULL,
  pthr = 1e-06,
  maxhits = 3
)

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.

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


chr1swallace/coloc documentation built on June 10, 2021, 8:38 p.m.