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Build a ColocResult

Source: R/ColocResult.R
ColocResult.Rd

Assemble a ColocResult from a pair-level table and the per-pair variant tables that go with it. Callers normally get one from colocPipeline rather than building it directly.

Usage

ColocResult(pairs, variants, ldSketch = NULL)

Arguments

pairs

A data frame with one row per tested pair, carrying at least the identity columns (study, context, trait, method, gwasStudy, gwasMethod), blockId, qtlCs, gwasCs, nSnps and PP.H0.abf through PP.H4.abf.

variants

A list, parallel to pairs' rows, of per-pair data frames with a variant_id column and a SNP.PP.H4 column.

ldSketch

Optional genotype panel (see readGenotypes) for the LD reference, used by getColocCredibleSets to compute purity.

Value

A ColocResult.

Examples

pairs <- data.frame(
    study = "s1", context = "c1", trait = "g1", method = "susie",
    gwasStudy = "G1", gwasMethod = "susie", blockId = "chr1_1_1000",
    qtlCs = 1L, gwasCs = 1L, nSnps = 2L,
    PP.H0.abf = 0.1, PP.H1.abf = 0.1, PP.H2.abf = 0.1,
    PP.H3.abf = 0.1, PP.H4.abf = 0.6
)
variants <- list(data.frame(
    variant_id = c("chr1:100:A:G", "chr1:200:C:T"),
    SNP.PP.H4 = c(0.7, 0.3)
))
ColocResult(pairs, variants)
#> ColocResult with 1 colocalized pair(s)
#>   QTL studies : s1 
#>   GWAS studies: G1 
#>   variants    : 2 across all pairs
#>   max PP.H4   : 0.6