coloc.process: Post process a coloc.details result using masking

In chr1swallace/coloc: Colocalisation Tests of Two Genetic Traits

Description

Internal helper function

Usage

coloc.process(
  obj,
  hits1 = NULL,
  hits2 = NULL,
  LD = NULL,
  r2thr = 0.01,
  p1 = 1e-04,
  p2 = 1e-04,
  p12 = 1e-06,
  LD1 = LD,
  LD2 = LD,
  mode = c("iterative", "allbutone")
)

Arguments

obj	object returned by coloc.detail()
hits1	lead snps for trait 1. If length > 1, will use masking
hits2	lead snps for trait 2. If length > 1, will use masking
LD	named LD matrix (for masking)
r2thr	r2 threshold at which to mask
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
LD1	named LD matrix (for masking) for trait 1 only
LD2	named LD matrix (for masking) for trait 2 only
mode	either "iterative" (default) - successively condition on signals or "allbutone" - find all putative signals and condition on all but one of them in each analysis

Value

data.table of coloc results

Author(s)

Chris Wallace

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