enloc Colocalisation Probabilities For One Signal Cluster

The quantities fastenloc reports for a single eQTL signal cluster, given the GWAS Bayes factors and the eQTL PIPs over the same variants.

Both parameterisations are returned because they come from one computation: rcp is ppH4 and lcp is ppH3 + ppH4.

Usage

enlocClusterProbabilities(
  gwasLog10Bf,
  qtlPip,
  pi1e,
  pi1ne,
  p12 = 0,
  applyFloor = FALSE
)

Arguments

gwasLog10Bf

Numeric vector of per-variant GWAS log10 Bayes factors.

qtlPip

Numeric vector of per-variant eQTL PIPs, same length and order.

pi1e

Prior probability of GWAS causality for a variant that is a causal eQTL, expit(a0 + a1).

pi1ne

The same for a variant that is not, expit(a0).

p12

Prior probability of colocalisation, used only for the small-probability floor fastenloc applies to each SNP-level term.

applyFloor

Logical. Apply that floor. fastenloc skips it on the summary-statistics path, where not all variants are present.

Value

A list with ppH0 to ppH4, rcp, lcp and scp (the per-variant colocalisation probabilities whose sum is rcp).

Examples

enlocClusterProbabilities(
  gwasLog10Bf = c(2, 0.1, 0.1),
  qtlPip = c(0.7, 0.2, 0.05),
  pi1e = 0.02,
  pi1ne = 0.001
)
#> $ppH0
#> [1] 0.0206496
#> 
#> $ppH1
#> [1] 0.002119072
#> 
#> $ppH2
#> [1] 0.3848805
#> 
#> $ppH3
#> [1] 0.01098098
#> 
#> $ppH4
#> [1] 0.5813699
#> 
#> $rcp
#> [1] 0.5813699
#> 
#> $lcp
#> [1] 0.5923508
#> 
#> $scp
#> [1] 0.5787676370 0.0020817865 0.0005204466
#>