Post process a coloc.details result using masking

Source: R/split.R

Internal helper function

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

Chris Wallace