Per-credible-set summary of a fine-mapping result

One row per credible set (at a given coverage) with its size, purity, prior variance, log Bayes factor, and lead variant – the per-CS complement to the per-variant getCs. Replaces the legacy per-effect `effect.tsv`.

Usage

getCredibleSetSummary(x, ...)

# S4 method for class 'FineMappingResultBase'
getCredibleSetSummary(x, coverage = 0.95, ...)

Arguments

x

A FineMappingRow or FineMappingResultBase.

...

Ignored.

coverage

Credible-set coverage to summarise. Default 0.95.

Value

A tibble: cs, effect_id, coverage, n_variants, purity_min, purity_mean, V, cs_log10bf (strongest member logBF), cs_log_bf (true per-effect single-effect log Bayes factor), cs_pip (summed member PIP = inclusion mass captured), cs_mean_effect (mean posterior conditional effect), lead_variant, lead_pip (the collection method also carries the entry identity columns).

See also

getCs, getTopLoci

Examples

data(qtlFineMappingExample)
getCredibleSetSummary(qtlFineMappingExample)
#> # A tibble: 1 × 18
#>   study   context   trait  blockId method cs      effect_id coverage n_variants
#>   <chr>   <chr>     <chr>  <chr>   <chr>  <chr>   <chr>        <dbl>      <int>
#> 1 study_1 context_1 gene_1 NA      susie  susie_1 L1            0.95         42
#> # ℹ 9 more variables: purity_min <dbl>, purity_mean <dbl>, V <dbl>,
#> #   cs_log10bf <dbl>, cs_log_bf <dbl>, cs_pip <dbl>, cs_mean_effect <dbl>,
#> #   lead_variant <chr>, lead_pip <dbl>