Coerce a ColocResult to a data frame

Returns the pair-level view, which is the flat table colocPipeline() used to return directly. Provided so existing consumers keep working; new code should call the view it actually wants (see colocViews).

Usage

# S4 method for class 'ColocResult'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x

A ColocResult.

row.names, optional

Ignored; present for generic compatibility.

...

Ignored.

Value

A data frame with one row per tested pair.

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)
))
as.data.frame(ColocResult(pairs, variants))
#>   study context trait method gwasStudy gwasMethod     blockId qtlCs gwasCs
#> 1    s1      c1    g1  susie        G1      susie chr1_1_1000     1      1
#>   nSnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
#> 1     2       0.1       0.1       0.1       0.1       0.6